>>> Unpacking source... * subversion update start --> * repository: http://coot.googlecode.com/svn/trunk At revision 2293. * working copy: /home/data/svn-src//coot/trunk >>> Unpacking greg-data.tar.gz to /home/data/svn-src/coot/trunk >>> Source unpacked in /var/tmp/portage/sci-chemistry/coot-9999/work >>> Preparing source in /var/tmp/portage/sci-chemistry/coot-9999/work ... * Applying 9999-as-needed.patch ...  [ ok ] * Applying link-against-guile-gtk-properly.patch ...  [ ok ] * Applying fix-namespace-error.patch ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-chemistry/coot-9999/work' ... * Running aclocal -I macros ...  [ ok ] * Running libtoolize --copy --force --install --automake ...  [ ok ] * Running aclocal -I macros ...  [ ok ] * Running autoconf ...  [ ok ] * Running automake --add-missing --copy ...  [ ok ] * Running elibtoolize in: * Applying sed-1.5.6.patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/coot-9999/work ... * econf: updating config.sub with /usr/share/gnuconfig/config.sub * econf: updating config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --includedir=${prefix}/include/coot --with-gtkcanvas-prefix=/usr --with-clipper-prefix=/usr --with-mmdb-prefix=/usr --with-ssmlib-prefix=/usr --with-gtkgl-prefix=/usr --with-guile --with-python=/usr --with-guile-gtk --with-gtk2 --with-pygtk checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking for library containing strerror... none required checking for i686-pc-linux-gnu-gcc... (cached) i686-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... (cached) yes checking whether i686-pc-linux-gnu-gcc accepts -g... (cached) yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed checking dependency style of i686-pc-linux-gnu-gcc... (cached) gcc3 checking for i686-pc-linux-gnu-gcc... (cached) i686-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... (cached) yes checking whether i686-pc-linux-gnu-gcc accepts -g... (cached) yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed checking dependency style of i686-pc-linux-gnu-gcc... (cached) gcc3 checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether i686-pc-linux-gnu-g++ accepts -g... yes checking dependency style of i686-pc-linux-gnu-g++... gcc3 checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by i686-pc-linux-gnu-gcc... /usr/i686-pc-linux-gnu/bin/ld checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 805306365 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/i686-pc-linux-gnu/bin/ld option to reload object files... -r checking for i686-pc-linux-gnu-objdump... i686-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... (cached) yes checking whether i686-pc-linux-gnu-g++ accepts -g... (cached) yes checking dependency style of i686-pc-linux-gnu-g++... (cached) gcc3 checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E checking for objdir... .libs checking if i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if i686-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if i686-pc-linux-gnu-gcc static flag -static works... yes checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes checking if i686-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld used by i686-pc-linux-gnu-g++... /usr/i686-pc-linux-gnu/bin/ld checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking for i686-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC checking if i686-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes checking if i686-pc-linux-gnu-g++ static flag -static works... yes checking if i686-pc-linux-gnu-g++ supports -c -o file.o... yes checking if i686-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for i686-pc-linux-gnu-ranlib... (cached) i686-pc-linux-gnu-ranlib checking sys/stdtypes.h usability... no checking sys/stdtypes.h presence... no checking for sys/stdtypes.h... no checking if this is MINGW on Windows... no checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 1.3... yes checking for i686-pc-linux-gnu-pkg-config... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GTK... yes checking for GNOME_CANVAS... yes checking for pkg-config... /usr/bin/pkg-config checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) checking for GLUT... yes checking for MMDB... yes checking for SSMLib... /usr checking for Clipper... yes Congratulations, you are using Guile checking for guile... /usr/bin/guile checking for guile-config... /usr/bin/guile-config checking for guile-tools... /usr/bin/guile-tools checking libguile compile flags... -pthread checking libguile link flags... -pthread -lguile -lltdl -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -lgmp -lcrypt -lm -lltdl checking for Guile Goosh... yes checking for net-hhtp... WARNING: (net http client): imported module (net http message) overrides core binding `version' yes checking for Guile-Lib... yes checking for guile-gui... yes checking GUILE_VERSION: 1.8 checking for Python... checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes Cool, using Python checking for PYGTK... yes Good we have pygtk checking for guile-gtk... checking libglade... yes Not using database checking build type... which: no rpm in (/usr/lib/ccache/bin:/usr/lib/portage/bin/ebuild-helpers:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/4.4.1:/opt/vmware/server/bin:/opt/vmware/vix/bin:/data/scripts) Linux-GenuineIntel---python-gtk2 configure: creating ./config.status config.status: creating Makefile config.status: creating macros/Makefile config.status: creating scheme/Makefile config.status: creating python/Makefile config.status: creating compat/Makefile config.status: creating coot-utils/Makefile config.status: creating ccp4mg-utils/Makefile config.status: creating coords/Makefile config.status: creating db-main/Makefile config.status: creating density-contour/Makefile config.status: creating surface/Makefile config.status: creating coot-surface/Makefile config.status: creating angles/Makefile config.status: creating atom-utils/Makefile config.status: creating mini-mol/Makefile config.status: creating skeleton/Makefile config.status: creating ligand/Makefile config.status: creating geometry/Makefile config.status: creating ideal/Makefile config.status: creating build/Makefile config.status: creating analysis/Makefile config.status: creating high-res/Makefile config.status: creating sequence-view/Makefile config.status: creating tw/Makefile config.status: creating cootaneer/Makefile config.status: creating greg-tests/Makefile config.status: creating python-tests/Makefile config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/coot config.status: creating setup/coot.sh config.status: creating setup/coot.csh config.status: creating python/coot_load_modules.py config.status: creating rama-data/Makefile config.status: creating auxil/Makefile config.status: creating auxil/catcheck/Makefile config.status: creating auxil/rama/Makefile config.status: creating auxil/sec-str/Makefile config.status: creating auxil/strand-analysis/Makefile config.status: creating auxil/vectors/Makefile config.status: executing depfiles commands config.status: executing libtool commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/coot-9999/work ... /var/tmp/portage/sci-chemistry/coot-9999/work/src /var/tmp/portage/sci-chemistry/coot-9999/work make -j5 -l3 coot_wrap_python.cc swig -o coot_wrap_python_pre.cc -DCOOT_USE_GTK2_INTERFACE -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -I../src -shadow -python -c++ ../src/coot.i cp coot_wrap_python_pre.cc coot_wrap_python.cc make -j5 -l3 coot_wrap_guile.cc swig -o coot_wrap_guile_pre.cc -DCOOT_USE_GTK2_INTERFACE -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -I../src -guile -c++ ../src/coot.i sh ../src/post-process-coot-wrap-guile.sh `/usr/bin/guile-config --version 2>&1 | awk '{print $NF}'` coot_wrap_guile_pre.cc coot_wrap_guile.cc sed -e s/SCM_STRING_CHARS/scm_to_locale_string/ -e s/static char .gswig_const_COOT_SCHEME_DIR/static const char *gswig_const_COOT_SCHEME_DIR/ coot_wrap_guile_pre.cc coot_wrap_guile.cc /var/tmp/portage/sci-chemistry/coot-9999/work make -j5 -l3 Making all in auxil make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil' Making all in catcheck make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/catcheck' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/catcheck' Making all in rama make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/rama' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/rama' Making all in sec-str make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/sec-str' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/sec-str' Making all in strand-analysis make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/strand-analysis' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/strand-analysis' Making all in vectors make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/vectors' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil/vectors' make[2]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil' make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/auxil' Making all in scheme make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/scheme' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/scheme' Making all in python make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/python' python ../python/python_coot_docs.py make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/python' Making all in macros make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/macros' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/macros' Making all in compat make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/compat' /bin/sh ../libtool --tag=CC --mode=compile i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -fPIC -DPIC -o .libs/getopt.o libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o >/dev/null 2>&1 mv -f .deps/getopt.Tpo .deps/getopt.Plo /bin/sh ../libtool --tag=CC --mode=compile i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c -o getopt1.lo getopt1.c libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -fPIC -DPIC -o .libs/getopt1.o libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -o getopt1.o >/dev/null 2>&1 mv -f .deps/getopt1.Tpo .deps/getopt1.Plo /bin/sh ../libtool --tag=CC --mode=link i686-pc-linux-gnu-gcc -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-compat.la -rpath /usr/lib getopt.lo getopt1.lo libtool: link: i686-pc-linux-gnu-gcc -shared .libs/getopt.o .libs/getopt1.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-compat.so.0 -o .libs/libcoot-compat.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-compat.so.0" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-compat.so" && ln -s "libcoot-compat.so.0.0.0" "libcoot-compat.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-compat.a getopt.o getopt1.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-compat.a libtool: link: ( cd ".libs" && rm -f "libcoot-compat.la" && ln -s "../libcoot-compat.la" "libcoot-compat.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/compat' Making all in coot-utils make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c -o coot-utils.lo coot-utils.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c coot-utils.cc -fPIC -DPIC -o .libs/coot-utils.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c coot-utils.cc -o coot-utils.o >/dev/null 2>&1 mv -f .deps/coot-utils.Tpo .deps/coot-utils.Plo /bin/sh ../libtool --tag=CXX --mode=compile 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test-shelx-reader.o -MD -MP -MF .deps/test-shelx-reader.Tpo -c -o test-shelx-reader.o test-shelx-reader.cc mv -f .deps/test-shelx-reader.Tpo .deps/test-shelx-reader.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../geometry -I../compat -I../mini-mol -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DUSE_GUILE -DUSE_PYTHON -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT test-utils.o -MD -MP -MF .deps/test-utils.Tpo -c -o test-utils.o test-utils.cc mv -f .deps/test-utils.Tpo .deps/test-utils.Po /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-map-utils.la -rpath /usr/lib coot-map-utils.lo peak-search.lo trim.lo xmap-stats.lo -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/coot-map-utils.o .libs/peak-search.o .libs/trim.o .libs/xmap-stats.o -L/usr/lib /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c -L/usr /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-map-utils.so.0 -o .libs/libcoot-map-utils.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-map-utils.so.0" && ln -s "libcoot-map-utils.so.0.0.0" "libcoot-map-utils.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-map-utils.so" && ln -s "libcoot-map-utils.so.0.0.0" "libcoot-map-utils.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-map-utils.a coot-map-utils.o peak-search.o trim.o xmap-stats.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-map-utils.a libtool: link: ( cd ".libs" && rm -f "libcoot-map-utils.la" && ln -s "../libcoot-map-utils.la" "libcoot-map-utils.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-coord-extras.la -rpath /usr/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/coot-coord-extras.o .libs/coot-coord-lsq.o .libs/coot-tree-extras.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 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"libcoot-coord-extras.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-map-heavy.la -rpath /usr/lib coot-map-heavy.lo coot-fffear.lo -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/coot-map-heavy.o .libs/coot-fffear.o -Wl,-rpath -Wl,/usr/lib/blas/threaded-atlas -Wl,-rpath -Wl,/usr/lib/blas/threaded-atlas -L/usr/lib /usr/lib/libgsl.so -L/usr/lib/blas/threaded-atlas /usr/lib/blas/threaded-atlas/libcblas.so -lcblas /usr/lib/libatlas.so -lpthread -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 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-L/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs -L/usr/lib -L/usr ./.libs/libcoot-coord-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-shelx.so.0 -o .libs/libcoot-shelx.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-shelx.so.0" && ln -s "libcoot-shelx.so.0.0.0" "libcoot-shelx.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-shelx.so" && ln -s "libcoot-shelx.so.0.0.0" "libcoot-shelx.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-shelx.a coot-shelx-ins.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-shelx.a libtool: link: ( cd ".libs" && rm -f "libcoot-shelx.la" && ln -s "../libcoot-shelx.la" "libcoot-shelx.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o testshelxreader test-shelx-reader.o ./libcoot-shelx.la ./libcoot-utils.la -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott 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-floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o testcootutils test-utils.o ./libcoot-shelx.la ./libcoot-utils.la -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/testcootutils test-utils.o ./.libs/libcoot-shelx.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so ./.libs/libcoot-utils.so /usr/lib/libmmdb.so -lm make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils' Making all in surface make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/surface' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXSphereElement.lo -MD -MP -MF .deps/CXXSphereElement.Tpo -c -o 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-DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXSphereElement.lo -MD -MP -MF .deps/CXXSphereElement.Tpo -c CXXSphereElement.cpp -o CXXSphereElement.o >/dev/null 2>&1 mv -f .deps/CXXSphereElement.Tpo .deps/CXXSphereElement.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 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.libs/CXXQADSurfaceStaticData.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXQADSurfaceStaticData.lo -MD -MP -MF .deps/CXXQADSurfaceStaticData.Tpo -c CXXQADSurfaceStaticData.cpp -o CXXQADSurfaceStaticData.o >/dev/null 2>&1 mv -f .deps/CXXQADSurfaceStaticData.Tpo .deps/CXXQADSurfaceStaticData.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c -o CXXSpace.lo CXXSpace.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -fPIC -DPIC -o .libs/CXXSpace.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXSpace.lo -MD -MP -MF .deps/CXXSpace.Tpo -c CXXSpace.cpp -o CXXSpace.o >/dev/null 2>&1 mv -f .deps/CXXSpace.Tpo .deps/CXXSpace.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXCircle.lo -MD -MP -MF .deps/CXXCircle.Tpo -c -o CXXCircle.lo CXXCircle.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXCircle.lo -MD -MP -MF .deps/CXXCircle.Tpo -c CXXCircle.cpp -fPIC -DPIC -o .libs/CXXCircle.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXCircle.lo -MD -MP -MF .deps/CXXCircle.Tpo -c CXXCircle.cpp -o CXXCircle.o >/dev/null 2>&1 mv -f .deps/CXXCircle.Tpo .deps/CXXCircle.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXSphereNode.lo -MD -MP -MF .deps/CXXSphereNode.Tpo -c -o CXXSphereNode.lo CXXSphereNode.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXSphereNode.lo -MD -MP -MF .deps/CXXSphereNode.Tpo -c CXXSphereNode.cpp -fPIC -DPIC -o .libs/CXXSphereNode.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXSphereNode.lo -MD -MP -MF .deps/CXXSphereNode.Tpo -c CXXSphereNode.cpp -o CXXSphereNode.o >/dev/null 2>&1 mv -f .deps/CXXSphereNode.Tpo .deps/CXXSphereNode.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c -o CXXChargeTable.lo CXXChargeTable.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c CXXChargeTable.cpp -fPIC -DPIC -o .libs/CXXChargeTable.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CXXChargeTable.lo -MD -MP -MF .deps/CXXChargeTable.Tpo -c CXXChargeTable.cpp -o CXXChargeTable.o >/dev/null 2>&1 mv -f .deps/CXXChargeTable.Tpo .deps/CXXChargeTable.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libccp4mg-surface.la -rpath /usr/lib CXXSphereElement.lo CXXChargeTable.lo CXXSphereNode.lo CXXCircle.lo CXXSphereTriangle.lo CXXCircleNode.lo CXXSphereTriangleEdge.lo CXXCoord.lo CXXSurface.lo CXXCreator.lo CXXSurfaceVertex.lo CXXException.lo CXXTorusElement.lo CXXFFTSolventMap.lo CXXTorusNode.lo CXXFortranFile.lo CXXNewHood.lo CXXTriangle.lo CXXNode.lo CXXQADSurface.lo CXXQADSurfaceStaticData.lo CXXSpace.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/CXXSphereElement.o .libs/CXXChargeTable.o .libs/CXXSphereNode.o .libs/CXXCircle.o .libs/CXXSphereTriangle.o .libs/CXXCircleNode.o .libs/CXXSphereTriangleEdge.o .libs/CXXCoord.o .libs/CXXSurface.o .libs/CXXCreator.o .libs/CXXSurfaceVertex.o .libs/CXXException.o .libs/CXXTorusElement.o .libs/CXXFFTSolventMap.o .libs/CXXTorusNode.o .libs/CXXFortranFile.o .libs/CXXNewHood.o .libs/CXXTriangle.o .libs/CXXNode.o .libs/CXXQADSurface.o .libs/CXXQADSurfaceStaticData.o .libs/CXXSpace.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libccp4mg-surface.so.0 -o .libs/libccp4mg-surface.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so.0" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so.0") libtool: link: (cd ".libs" && rm -f "libccp4mg-surface.so" && ln -s "libccp4mg-surface.so.0.0.0" "libccp4mg-surface.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libccp4mg-surface.a CXXSphereElement.o CXXChargeTable.o CXXSphereNode.o CXXCircle.o CXXSphereTriangle.o CXXCircleNode.o CXXSphereTriangleEdge.o CXXCoord.o CXXSurface.o CXXCreator.o CXXSurfaceVertex.o CXXException.o CXXTorusElement.o CXXFFTSolventMap.o CXXTorusNode.o CXXFortranFile.o CXXNewHood.o CXXTriangle.o CXXNode.o CXXQADSurface.o CXXQADSurfaceStaticData.o CXXSpace.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libccp4mg-surface.a libtool: link: ( cd ".libs" && rm -f "libccp4mg-surface.la" && ln -s "../libccp4mg-surface.la" "libccp4mg-surface.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/surface' Making all in coot-surface make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/coot-surface' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c -o coot-surface.lo coot-surface.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc -fPIC -DPIC -o .libs/coot-surface.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-surface.lo -MD -MP -MF .deps/coot-surface.Tpo -c coot-surface.cc -o coot-surface.o >/dev/null 2>&1 mv -f .deps/coot-surface.Tpo .deps/coot-surface.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c -o rgbreps.lo rgbreps.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -fPIC -DPIC -o .libs/rgbreps.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../surface -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT rgbreps.lo -MD -MP -MF .deps/rgbreps.Tpo -c rgbreps.cc -o rgbreps.o >/dev/null 2>&1 mv -f .deps/rgbreps.Tpo .deps/rgbreps.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-surface.la -rpath /usr/lib coot-surface.lo rgbreps.lo ../surface/libccp4mg-surface.la libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/coot-surface.o .libs/rgbreps.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/surface/.libs ../surface/.libs/libccp4mg-surface.so -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-surface.so.0" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-surface.so" && ln -s "libcoot-surface.so.0.0.0" "libcoot-surface.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-surface.a coot-surface.o rgbreps.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-surface.a libtool: link: ( cd ".libs" && rm -f "libcoot-surface.la" && ln -s "../libcoot-surface.la" "libcoot-surface.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/coot-surface' Making all in atom-utils make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/atom-utils' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DHAVE_GSL -I/usr/include -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT atom-utils.lo -MD -MP -MF .deps/atom-utils.Tpo -c -o atom-utils.lo atom-utils.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DHAVE_GSL -I/usr/include -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT atom-utils.lo -MD -MP -MF .deps/atom-utils.Tpo -c atom-utils.cc -fPIC -DPIC -o .libs/atom-utils.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DHAVE_GSL -I/usr/include -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT atom-utils.lo -MD -MP -MF .deps/atom-utils.Tpo -c atom-utils.cc -o atom-utils.o >/dev/null 2>&1 mv -f .deps/atom-utils.Tpo .deps/atom-utils.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-atomutils.la -rpath /usr/lib atom-utils.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/atom-utils.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-atomutils.so.0 -o .libs/libcoot-atomutils.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-atomutils.so.0" && ln -s "libcoot-atomutils.so.0.0.0" "libcoot-atomutils.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-atomutils.so" && ln -s "libcoot-atomutils.so.0.0.0" "libcoot-atomutils.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-atomutils.a atom-utils.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-atomutils.a libtool: link: ( cd ".libs" && rm -f "libcoot-atomutils.la" && ln -s "../libcoot-atomutils.la" "libcoot-atomutils.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/atom-utils' Making all in skeleton make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/skeleton' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c -o dm-utils.lo dm-utils.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc -fPIC -DPIC -o .libs/dm-utils.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT dm-utils.lo -MD -MP -MF .deps/dm-utils.Tpo -c dm-utils.cc -o dm-utils.o >/dev/null 2>&1 mv -f .deps/dm-utils.Tpo .deps/dm-utils.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c -o BuildCas.lo BuildCas.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -fPIC -DPIC -o .libs/BuildCas.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT BuildCas.lo -MD -MP -MF .deps/BuildCas.Tpo -c BuildCas.cc -o BuildCas.o >/dev/null 2>&1 mv -f .deps/BuildCas.Tpo .deps/BuildCas.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c -o graphical_skel.lo graphical_skel.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc -fPIC -DPIC -o .libs/graphical_skel.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../angles -I../atom-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphical_skel.lo -MD -MP -MF .deps/graphical_skel.Tpo -c graphical_skel.cc -o graphical_skel.o >/dev/null 2>&1 mv -f .deps/graphical_skel.Tpo .deps/graphical_skel.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-skeleton.la -rpath /usr/lib dm-utils.lo graphical_skel.lo BuildCas.lo ../atom-utils/libcoot-atomutils.la libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/atom-utils/.libs ../atom-utils/.libs/libcoot-atomutils.so -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so.0" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-skeleton.so" && ln -s "libcoot-skeleton.so.0.0.0" "libcoot-skeleton.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-skeleton.a dm-utils.o graphical_skel.o BuildCas.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-skeleton.a libtool: link: ( cd ".libs" && rm -f "libcoot-skeleton.la" && ln -s "../libcoot-skeleton.la" "libcoot-skeleton.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/skeleton' Making all in ccp4mg-utils make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/ccp4mg-utils' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c -o geomutil.lo geomutil.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -fPIC -DPIC -o .libs/geomutil.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -o geomutil.o >/dev/null 2>&1 mv -f .deps/geomutil.Tpo .deps/geomutil.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c -o quat.lo quat.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -fPIC -DPIC -o .libs/quat.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -o quat.o >/dev/null 2>&1 mv -f .deps/quat.Tpo .deps/quat.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c -o ppmutil.lo ppmutil.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc -fPIC -DPIC -o .libs/ppmutil.o ppmutil.cc: In member function ‘void image_info::writewbmp(const char*) const’: ppmutil.cc:2551: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘unsigned int’ libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc -o ppmutil.o >/dev/null 2>&1 mv -f .deps/ppmutil.Tpo .deps/ppmutil.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -fPIC -DPIC -o .libs/matrix.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -o matrix.o >/dev/null 2>&1 mv -f .deps/matrix.Tpo .deps/matrix.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c -o cartesian.lo cartesian.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -fPIC -DPIC -o .libs/cartesian.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -o cartesian.o >/dev/null 2>&1 mv -f .deps/cartesian.Tpo .deps/cartesian.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c -o mgtree.lo mgtree.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -fPIC -DPIC -o .libs/mgtree.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -o mgtree.o >/dev/null 2>&1 mv -f .deps/mgtree.Tpo .deps/mgtree.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libccp4mg-utils.la -rpath /usr/lib geomutil.lo mgtree.lo cartesian.lo matrix.lo quat.lo ppmutil.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/geomutil.o .libs/mgtree.o .libs/cartesian.o .libs/matrix.o .libs/quat.o .libs/ppmutil.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libccp4mg-utils.so.0 -o .libs/libccp4mg-utils.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so.0" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so.0") libtool: link: (cd ".libs" && rm -f "libccp4mg-utils.so" && ln -s "libccp4mg-utils.so.0.0.0" "libccp4mg-utils.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libccp4mg-utils.a geomutil.o mgtree.o cartesian.o matrix.o quat.o ppmutil.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libccp4mg-utils.a libtool: link: ( cd ".libs" && rm -f "libccp4mg-utils.la" && ln -s "../libccp4mg-utils.la" "libccp4mg-utils.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/ccp4mg-utils' Making all in density-contour make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/density-contour' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c -o Vectors.lo Vectors.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c Vectors.cpp -fPIC -DPIC -o .libs/Vectors.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT Vectors.lo -MD -MP -MF .deps/Vectors.Tpo -c Vectors.cpp -o Vectors.o >/dev/null 2>&1 mv -f .deps/Vectors.Tpo .deps/Vectors.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c -o CIsoSurface.lo CIsoSurface.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c CIsoSurface.cpp -fPIC -DPIC -o .libs/CIsoSurface.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CIsoSurface.lo -MD -MP -MF .deps/CIsoSurface.Tpo -c CIsoSurface.cpp -o CIsoSurface.o >/dev/null 2>&1 mv -f .deps/CIsoSurface.Tpo .deps/CIsoSurface.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-isosurface.la -rpath /usr/lib Vectors.lo CIsoSurface.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/Vectors.o .libs/CIsoSurface.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so.0" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-isosurface.so" && ln -s "libcoot-isosurface.so.0.0.0" "libcoot-isosurface.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-isosurface.a Vectors.o CIsoSurface.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-isosurface.a libtool: link: ( cd ".libs" && rm -f "libcoot-isosurface.la" && ln -s "../libcoot-isosurface.la" "libcoot-isosurface.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/density-contour' Making all in mini-mol make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c -o mini-mol.lo mini-mol.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -fPIC -DPIC -o .libs/mini-mol.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -o mini-mol.o >/dev/null 2>&1 mv -f .deps/mini-mol.Tpo .deps/mini-mol.Plo i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT testminimol.o -MD -MP -MF .deps/testminimol.Tpo -c -o testminimol.o testminimol.cc mv -f .deps/testminimol.Tpo .deps/testminimol.Po /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c -o atom-quads.lo atom-quads.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -fPIC -DPIC -o .libs/atom-quads.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -o atom-quads.o >/dev/null 2>&1 mv -f .deps/atom-quads.Tpo .deps/atom-quads.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c -o mini-mol-utils.lo mini-mol-utils.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -fPIC -DPIC -o .libs/mini-mol-utils.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -o mini-mol-utils.o >/dev/null 2>&1 mv -f .deps/mini-mol-utils.Tpo .deps/mini-mol-utils.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-mini-mol.la -rpath /usr/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo ../coot-utils/libcoot-coord-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs ../coot-utils/.libs/libcoot-coord-utils.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so.0" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-mini-mol.a mini-mol.o mini-mol-utils.o atom-quads.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-mini-mol.a libtool: link: ( cd ".libs" && rm -f "libcoot-mini-mol.la" && ln -s "../libcoot-mini-mol.la" "libcoot-mini-mol.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o testminimol testminimol.o libcoot-mini-mol.la -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/testminimol testminimol.o ./.libs/libcoot-mini-mol.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol' Making all in coords make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/coords' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c -o Bond_lines.lo Bond_lines.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c Bond_lines.cc -fPIC -DPIC -o .libs/Bond_lines.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT Bond_lines.lo -MD -MP -MF .deps/Bond_lines.Tpo -c Bond_lines.cc -o Bond_lines.o >/dev/null 2>&1 mv -f .deps/Bond_lines.Tpo .deps/Bond_lines.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c -o utils.lo utils.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.cc -fPIC -DPIC -o .libs/utils.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT utils.lo -MD -MP -MF .deps/utils.Tpo -c utils.cc -o utils.o >/dev/null 2>&1 mv -f .deps/utils.Tpo 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-DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cos-sin.lo -MD -MP -MF .deps/cos-sin.Tpo -c -o cos-sin.lo cos-sin.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cos-sin.lo -MD -MP -MF .deps/cos-sin.Tpo -c cos-sin.cc -fPIC -DPIC -o .libs/cos-sin.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cos-sin.lo -MD -MP -MF .deps/cos-sin.Tpo -c cos-sin.cc -o cos-sin.o >/dev/null 2>&1 mv -f 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-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT Cartesian.lo -MD -MP -MF .deps/Cartesian.Tpo -c Cartesian.cc -fPIC -DPIC -o .libs/Cartesian.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../skeleton -I../coot-utils -I../mini-mol -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT Cartesian.lo -MD -MP -MF .deps/Cartesian.Tpo -c Cartesian.cc -o Cartesian.o >/dev/null 2>&1 mv -f .deps/Cartesian.Tpo .deps/Cartesian.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-coords.la -rpath /usr/lib Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs ../coot-utils/.libs/libcoot-shelx.so -L/usr/lib -L/usr ../mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-coords.so.0" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-coords.so" && ln -s "libcoot-coords.so.0.0.0" "libcoot-coords.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-coords.a Bond_lines.o Cartesian.o cos-sin.o mmdb-extras.o utils.o mmdb.o mmdb-crystal.o Bond_lines_ext.o coot-close.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-coords.a libtool: link: ( cd ".libs" && rm -f "libcoot-coords.la" && ln -s "../libcoot-coords.la" "libcoot-coords.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/coords' Making all in angles make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/angles' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 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.deps/libcoot_AngleInfo_la-AngleInfo.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo `test -f 'AngleInfo-theta_2-autogen.cc' || echo './'`AngleInfo-theta_2-autogen.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c AngleInfo-theta_2-autogen.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c AngleInfo-theta_2-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o >/dev/null 2>&1 mv -f .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo `test -f 'AngleInfo-angle-torsions-autogen.cc' || echo './'`AngleInfo-angle-torsions-autogen.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c AngleInfo-angle-torsions-autogen.cc -fPIC -DPIC -o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -g -O1 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c AngleInfo-angle-torsions-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o >/dev/null 2>&1 mv -f .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -g -O1 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-AngleInfo.la -rpath /usr/lib libcoot_AngleInfo_la-AngleInfo.lo libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/libcoot_AngleInfo_la-AngleInfo.o .libs/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o .libs/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-AngleInfo.so.0 -o .libs/libcoot-AngleInfo.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so.0" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-AngleInfo.so" && ln -s "libcoot-AngleInfo.so.0.0.0" "libcoot-AngleInfo.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-AngleInfo.a libcoot_AngleInfo_la-AngleInfo.o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-AngleInfo.a libtool: link: ( cd ".libs" && rm -f "libcoot-AngleInfo.la" && ln -s "../libcoot-AngleInfo.la" "libcoot-AngleInfo.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/angles' Making all in db-main make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/db-main' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c -o db-main.lo db-main.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c db-main.cc -fPIC -DPIC -o .libs/db-main.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c db-main.cc -o db-main.o >/dev/null 2>&1 mv -f .deps/db-main.Tpo .deps/db-main.Plo i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT train-pepflip.o -MD -MP -MF .deps/train-pepflip.Tpo -c -o train-pepflip.o train-pepflip.cc mv -f .deps/train-pepflip.Tpo .deps/train-pepflip.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT testdbmain.o -MD -MP -MF .deps/testdbmain.Tpo -c -o testdbmain.o testdbmain.cc mv -f .deps/testdbmain.Tpo .deps/testdbmain.Po /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c -o db-strands.lo db-strands.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c db-strands.cc -fPIC -DPIC -o .libs/db-strands.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I../mini-mol -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c db-strands.cc -o db-strands.o >/dev/null 2>&1 mv -f .deps/db-strands.Tpo .deps/db-strands.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-db-main.la -rpath /usr/lib db-main.lo db-strands.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/db-main.o .libs/db-strands.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so.0" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-db-main.so" && ln -s "libcoot-db-main.so.0.0.0" "libcoot-db-main.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-db-main.a db-main.o db-strands.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-db-main.a libtool: link: ( cd ".libs" && rm -f "libcoot-db-main.la" && ln -s "../libcoot-db-main.la" "libcoot-db-main.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o testdbmain testdbmain.o libcoot-db-main.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/testdbmain testdbmain.o ./.libs/libcoot-db-main.so ../mini-mol/.libs/libcoot-mini-mol.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so ../coot-utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DDATADIR='"/usr/share"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o train-pepflip train-pepflip.o libcoot-db-main.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/train-pepflip train-pepflip.o ./.libs/libcoot-db-main.so ../mini-mol/.libs/libcoot-mini-mol.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so ../coot-utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/db-main' Making all in geometry make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/geometry' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c -o protein-geometry.lo protein-geometry.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c protein-geometry.cc -fPIC -DPIC -o .libs/protein-geometry.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c protein-geometry.cc -o protein-geometry.o >/dev/null 2>&1 mv -f .deps/protein-geometry.Tpo .deps/protein-geometry.Plo i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT test-read-components.o -MD -MP -MF .deps/test-read-components.Tpo -c -o test-read-components.o test-read-components.cc mv -f .deps/test-read-components.Tpo .deps/test-read-components.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT test-geometry.o -MD -MP -MF .deps/test-geometry.Tpo -c -o test-geometry.o test-geometry.cc mv -f .deps/test-geometry.Tpo .deps/test-geometry.Po /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c -o protein-geometry-mmdb.lo protein-geometry-mmdb.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c protein-geometry-mmdb.cc -fPIC -DPIC -o .libs/protein-geometry-mmdb.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coords -I../coot-utils -I../compat -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c protein-geometry-mmdb.cc -o protein-geometry-mmdb.o >/dev/null 2>&1 mv -f .deps/protein-geometry-mmdb.Tpo .deps/protein-geometry-mmdb.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-geometry.la -rpath /usr/lib protein-geometry.lo protein-geometry-mmdb.lo ../coot-utils/libcoot-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/protein-geometry.o .libs/protein-geometry-mmdb.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs ../coot-utils/.libs/libcoot-utils.so -L/usr/lib /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c -L/usr /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so.0" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-geometry.so" && ln -s "libcoot-geometry.so.0.0.0" "libcoot-geometry.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-geometry.a protein-geometry.o protein-geometry-mmdb.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-geometry.a libtool: link: ( cd ".libs" && rm -f "libcoot-geometry.la" && ln -s "../libcoot-geometry.la" "libcoot-geometry.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o test-geometry test-geometry.o ./libcoot-geometry.la libtool: link: i686-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/test-geometry test-geometry.o ./.libs/libcoot-geometry.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lm -lz -lpthread /usr/lib/libmmdb.so /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o test-read-components test-read-components.o ./libcoot-geometry.la libtool: link: i686-pc-linux-gnu-g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/test-read-components test-read-components.o ./.libs/libcoot-geometry.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lm -lz -lpthread /usr/lib/libmmdb.so make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/geometry' Making all in ideal make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/ideal' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT simple-restraint.lo -MD -MP -MF .deps/simple-restraint.Tpo -c -o simple-restraint.lo simple-restraint.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT simple-restraint.lo -MD -MP -MF .deps/simple-restraint.Tpo -c simple-restraint.cc -fPIC -DPIC -o .libs/simple-restraint.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT simple-restraint.lo -MD -MP -MF .deps/simple-restraint.Tpo -c simple-restraint.cc -o simple-restraint.o >/dev/null 2>&1 mv -f .deps/simple-restraint.Tpo .deps/simple-restraint.Plo i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT test-indexing.o -MD -MP -MF .deps/test-indexing.Tpo -c -o test-indexing.o test-indexing.cc mv -f .deps/test-indexing.Tpo .deps/test-indexing.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../coot-utils -I../mini-mol -I../geometry -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT with-geometry.o -MD -MP -MF .deps/with-geometry.Tpo -c -o with-geometry.o with-geometry.cc mv -f .deps/with-geometry.Tpo .deps/with-geometry.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 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.deps/richardson-rotamers.Tpo -c richardson-rotamers.cc -o richardson-rotamers.o >/dev/null 2>&1 mv -f .deps/richardson-rotamers.Tpo .deps/richardson-rotamers.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine 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richardson-rotamer.cc -o richardson-rotamer.o >/dev/null 2>&1 mv -f .deps/richardson-rotamer.Tpo .deps/richardson-rotamer.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT rotamer.lo -MD -MP -MF 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--tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT ligand-extras.lo -MD -MP -MF .deps/ligand-extras.Tpo -c -o ligand-extras.lo ligand-extras.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" 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-DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../ccp4mg-utils -I../mini-mol -I../geometry -I../ideal -I../coords -I../coot-utils -I../compat -I../db-main -DHAVE_GSL -I/usr/include -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT ligand-extras.lo -MD -MP -MF .deps/ligand-extras.Tpo -c ligand-extras.cc -o ligand-extras.o >/dev/null 2>&1 mv -f .deps/ligand-extras.Tpo .deps/ligand-extras.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer 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rm -f "libcoot-ligand.so.0" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-ligand.a ligand.o ligand-extras.o residue_by_phi_psi.o wiggly-ligand.o monomer-utils.o dunbrack.o chi-angles-autogen.o chi-angles.o helix-placement.o fast-ss-search.o rigid-body.o ideal-rna.o richardson-rotamers.o richardson-rotamer.o rotamer.o torsion-general.o rotamer-tables.o primitive-chi-angles.o dipole.o base-pairing.o backrub-rotamer.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-ligand.a libtool: link: ( cd ".libs" && rm -f "libcoot-ligand.la" && ln -s "../libcoot-ligand.la" "libcoot-ligand.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine 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/usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz /usr/lib/libmmdb.so /usr/lib/libgsl.so /usr/lib/blas/threaded-atlas/libcblas.so -lcblas /usr/lib/libatlas.so -lpthread -lm -Wl,-rpath -Wl,/usr/lib/blas/threaded-atlas /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o findwaters-real find-waters.o ./libcoot-ligand.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../db-main/libcoot-db-main.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-utils.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/findwaters-real find-waters.o ./.libs/libcoot-ligand.so -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-9999/work/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-extras.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-map-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-9999/work/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-9999/work/ccp4mg-utils/.libs/libccp4mg-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol/.libs/libcoot-mini-mol.so ../ccp4mg-utils/.libs/libccp4mg-utils.so ../db-main/.libs/libcoot-db-main.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-utils.so ../coot-utils/.libs/libcoot-shelx.so ../mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz /usr/lib/libmmdb.so /usr/lib/libgsl.so /usr/lib/blas/threaded-atlas/libcblas.so -lcblas /usr/lib/libatlas.so -lpthread -lm -Wl,-rpath -Wl,/usr/lib/blas/threaded-atlas make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/ligand' Making all in high-res make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/high-res' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 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i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../geometry -I../coords -I../ccp4mg-utils -I../mini-mol -I../ligand -I../coot-utils -I../compat -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -DHAVE_GSL -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-atom-graph.lo -MD -MP -MF .deps/coot-atom-graph.Tpo -c coot-atom-graph.cc -o coot-atom-graph.o >/dev/null 2>&1 mv -f .deps/coot-atom-graph.Tpo .deps/coot-atom-graph.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DHAVE_GSL -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-high-res.la -rpath /usr/lib high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../ligand/libcoot-ligand.la ../coot-utils/libcoot-map-utils.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/ligand/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/ideal/.libs -Wl,-rpath -Wl,/usr/lib/blas/threaded-atlas -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/coords/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/db-main/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/geometry/.libs -Wl,-rpath -Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/ccp4mg-utils/.libs -Wl,-rpath -Wl,/usr/lib/blas/threaded-atlas -L/var/tmp/portage/sci-chemistry/coot-9999/work/ideal/.libs -L/var/tmp/portage/sci-chemistry/coot-9999/work/coords/.libs -L/var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol/.libs -L/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-9999/work/db-main/.libs -L/var/tmp/portage/sci-chemistry/coot-9999/work/geometry/.libs 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.libs/libcoot-high-res.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so.0" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-high-res.a high-res.o coot-atom-graph.o residue-distortions.o sequence-assignment.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-high-res.a libtool: link: ( cd ".libs" && rm -f "libcoot-high-res.la" && ln -s "../libcoot-high-res.la" "libcoot-high-res.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/high-res' Making all in build make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/build' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" 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-I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT CalphaBuild.lo -MD -MP -MF .deps/CalphaBuild.Tpo -c CalphaBuild.cc -fPIC -DPIC -o .libs/CalphaBuild.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../angles -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT 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"libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-cabuild.so" && ln -s "libcoot-cabuild.so.0.0.0" "libcoot-cabuild.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-cabuild.a CalphaBuild.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-cabuild.a libtool: link: ( cd ".libs" && rm -f "libcoot-cabuild.la" && ln -s "../libcoot-cabuild.la" "libcoot-cabuild.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o testcabuild testcabuild.o ./libcoot-cabuild.la ../angles/libcoot-AngleInfo.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm libtool: 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python-tests make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/python-tests' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/python-tests' Making all in analysis make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/analysis' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c -o bfkurt.lo bfkurt.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c bfkurt.cc -fPIC -DPIC -o .libs/bfkurt.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../coot-utils -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c bfkurt.cc -o bfkurt.o >/dev/null 2>&1 mv -f .deps/bfkurt.Tpo .deps/bfkurt.Plo i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 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-Wl,/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs -L/var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs ../coot-utils/.libs/libcoot-coord-utils.so -L/usr/lib -L/usr /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so.0" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-analysis.a bfkurt.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-analysis.a libtool: link: ( cd ".libs" && rm -f "libcoot-analysis.la" && ln -s "../libcoot-analysis.la" "libcoot-analysis.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o bfactan bfactan.o libcoot-analysis.la ../coot-utils/libcoot-utils.la ../geometry/libcoot-geometry.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/bfactan bfactan.o ./.libs/libcoot-analysis.so -L/usr/lib -L/usr /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-utils.so ../geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/analysis' Making all in sequence-view make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/sequence-view' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR='"/usr/share/coot"' -DHAVE_GSL -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT sequence-view.lo -MD -MP -MF .deps/sequence-view.Tpo -c -o sequence-view.lo sequence-view.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR=\"/usr/share/coot\" -DHAVE_GSL -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT sequence-view.lo -MD -MP -MF .deps/sequence-view.Tpo -c sequence-view.cc -fPIC -DPIC -o .libs/sequence-view.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR=\"/usr/share/coot\" -DHAVE_GSL -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT sequence-view.lo -MD -MP -MF .deps/sequence-view.Tpo -c sequence-view.cc -o sequence-view.o >/dev/null 2>&1 mv -f .deps/sequence-view.Tpo .deps/sequence-view.Plo /bin/sh ../libtool --tag=CC --mode=compile i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT seq-view-interface.lo -MD -MP -MF .deps/seq-view-interface.Tpo -c -o seq-view-interface.lo seq-view-interface.c libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT seq-view-interface.lo -MD -MP -MF .deps/seq-view-interface.Tpo -c seq-view-interface.c -fPIC -DPIC -o .libs/seq-view-interface.o libtool: compile: i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -I../src -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DHAVE_SSMLIB -I/usr/include/ssm -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT seq-view-interface.lo -MD -MP -MF .deps/seq-view-interface.Tpo -c seq-view-interface.c -o seq-view-interface.o >/dev/null 2>&1 mv -f .deps/seq-view-interface.Tpo .deps/seq-view-interface.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DHAVE_GSL -I/usr/include -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-sequence-view.la -rpath /usr/lib sequence-view.lo seq-view-interface.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/sequence-view.o .libs/seq-view-interface.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-sequence-view.so.0 -o .libs/libcoot-sequence-view.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-sequence-view.so.0" && ln -s "libcoot-sequence-view.so.0.0.0" "libcoot-sequence-view.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-sequence-view.so" && ln -s "libcoot-sequence-view.so.0.0.0" "libcoot-sequence-view.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-sequence-view.a sequence-view.o seq-view-interface.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-sequence-view.a libtool: link: ( cd ".libs" && rm -f "libcoot-sequence-view.la" && ln -s "../libcoot-sequence-view.la" "libcoot-sequence-view.la" ) make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/sequence-view' Making all in tw make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/tw' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT tw.lo -MD -MP -MF .deps/tw.Tpo -c -o tw.lo tw.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT tw.lo -MD -MP -MF .deps/tw.Tpo -c tw.cc -fPIC -DPIC -o .libs/tw.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT tw.lo -MD -MP -MF .deps/tw.Tpo -c tw.cc -o tw.o >/dev/null 2>&1 mv -f .deps/tw.Tpo .deps/tw.Plo i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT tiddly.o -MD -MP -MF .deps/tiddly.Tpo -c -o tiddly.o tiddly.cc mv -f .deps/tiddly.Tpo .deps/tiddly.Po /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-tw.la -rpath /usr/lib tw.lo -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/tw.o /usr/lib/libgtk-x11-2.0.so /usr/lib/libgdk-x11-2.0.so /usr/lib/libatk-1.0.so -L/usr/lib /usr/lib/libgdk_pixbuf-2.0.so /usr/lib/libgio-2.0.so /usr/lib/libpangocairo-1.0.so /usr/lib/libpangoft2-1.0.so /usr/lib/libcairo.so /usr/lib/libpixman-1.so /usr/lib/libpng12.so /usr/lib/libXrender.so /usr/lib/libX11.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so /usr/lib/libpango-1.0.so /usr/lib/libfontconfig.so /usr/lib/libfreetype.so -lz /usr/lib/libexpat.so /usr/lib/libgobject-2.0.so /usr/lib/libgmodule-2.0.so -ldl /usr/lib/libglib-2.0.so -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcoot-tw.so.0 -o .libs/libcoot-tw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-tw.so.0" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-tw.so" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-tw.a tw.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-tw.a libtool: link: ( cd ".libs" && rm -f "libcoot-tw.la" && ln -s "../libcoot-tw.la" "libcoot-tw.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o coot-tiddly tiddly.o libcoot-tw.la libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/coot-tiddly tiddly.o ./.libs/libcoot-tw.so /usr/lib/libgtk-x11-2.0.so /usr/lib/libgdk-x11-2.0.so /usr/lib/libatk-1.0.so /usr/lib/libgdk_pixbuf-2.0.so /usr/lib/libgio-2.0.so /usr/lib/libpangocairo-1.0.so /usr/lib/libpangoft2-1.0.so /usr/lib/libcairo.so /usr/lib/libpixman-1.so /usr/lib/libpng12.so /usr/lib/libXrender.so /usr/lib/libX11.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so /usr/lib/libpango-1.0.so -lm /usr/lib/libfontconfig.so /usr/lib/libfreetype.so -lz /usr/lib/libexpat.so /usr/lib/libgobject-2.0.so /usr/lib/libgmodule-2.0.so -ldl /usr/lib/libglib-2.0.so make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/tw' Making all in cootaneer make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/cootaneer' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c -o buccaneer-lib.lo buccaneer-lib.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c buccaneer-lib.cpp -fPIC -DPIC -o .libs/buccaneer-lib.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c buccaneer-lib.cpp -o buccaneer-lib.o >/dev/null 2>&1 mv -f .deps/buccaneer-lib.Tpo .deps/buccaneer-lib.Plo i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cootaneer-demo.o -MD -MP -MF .deps/cootaneer-demo.Tpo -c -o cootaneer-demo.o cootaneer-demo.cpp mv -f .deps/cootaneer-demo.Tpo .deps/cootaneer-demo.Po /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c -o cootaneer-sequence.lo cootaneer-sequence.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c cootaneer-sequence.cpp -fPIC -DPIC -o .libs/cootaneer-sequence.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c cootaneer-sequence.cpp -o cootaneer-sequence.o >/dev/null 2>&1 mv -f .deps/cootaneer-sequence.Tpo .deps/cootaneer-sequence.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c -o buccaneer-sequence.lo buccaneer-sequence.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c buccaneer-sequence.cpp -fPIC -DPIC -o .libs/buccaneer-sequence.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c buccaneer-sequence.cpp -o buccaneer-sequence.o >/dev/null 2>&1 mv -f .deps/buccaneer-sequence.Tpo .deps/buccaneer-sequence.Plo /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c -o buccaneer-prot.lo buccaneer-prot.cpp libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c buccaneer-prot.cpp -fPIC -DPIC -o .libs/buccaneer-prot.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I/usr/include -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c buccaneer-prot.cpp -o buccaneer-prot.o >/dev/null 2>&1 mv -f .deps/buccaneer-prot.Tpo .deps/buccaneer-prot.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcootaneer.la -rpath /usr/lib buccaneer-lib.lo buccaneer-prot.lo buccaneer-sequence.lo cootaneer-sequence.lo -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/buccaneer-lib.o .libs/buccaneer-prot.o .libs/buccaneer-sequence.o .libs/cootaneer-sequence.o -L/usr/lib /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c -L/usr /usr/lib/libmmdb.so /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,-soname -Wl,libcootaneer.so.0 -o .libs/libcootaneer.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcootaneer.so.0" && ln -s "libcootaneer.so.0.0.0" "libcootaneer.so.0") libtool: link: (cd ".libs" && rm -f "libcootaneer.so" && ln -s "libcootaneer.so.0.0.0" "libcootaneer.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcootaneer.a buccaneer-lib.o buccaneer-prot.o buccaneer-sequence.o cootaneer-sequence.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcootaneer.a libtool: link: ( cd ".libs" && rm -f "libcootaneer.la" && ln -s "../libcootaneer.la" "libcootaneer.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o cootaneer-demo cootaneer-demo.o ./libcootaneer.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/cootaneer-demo cootaneer-demo.o ./.libs/libcootaneer.so -L/usr/lib -L/usr /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz -lpthread /usr/lib/libmmdb.so -lm make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/cootaneer' Making all in src make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/src' /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot_wrap_python.lo -MD -MP -MF .deps/coot_wrap_python.Tpo -c -o coot_wrap_python.lo coot_wrap_python.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot_wrap_python.lo -MD -MP -MF .deps/coot_wrap_python.Tpo -c coot_wrap_python.cc -fPIC -DPIC -o .libs/coot_wrap_python.o libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot_wrap_python.lo -MD -MP -MF .deps/coot_wrap_python.Tpo -c coot_wrap_python.cc -o coot_wrap_python.o >/dev/null 2>&1 mv -f .deps/coot_wrap_python.Tpo .deps/coot_wrap_python.Plo i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-inner-main.o -MD -MP -MF .deps/c-inner-main.Tpo -c -o c-inner-main.o c-inner-main.c mv -f .deps/c-inner-main.Tpo .deps/c-inner-main.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-build.o -MD -MP -MF .deps/c-interface-build.Tpo -c -o c-interface-build.o c-interface-build.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-build.cc:61: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-build.cc:26: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-build.cc:61: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-build.cc:26: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-build.Tpo .deps/c-interface-build.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-build-gui.o -MD -MP -MF .deps/c-interface-build-gui.Tpo -c -o c-interface-build-gui.o c-interface-build-gui.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-build-gui.cc:61: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-build-gui.cc:26: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-build-gui.cc:61: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-build-gui.cc:26: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-build-gui.Tpo .deps/c-interface-build-gui.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-database.o -MD -MP -MF .deps/c-interface-database.Tpo -c -o c-interface-database.o c-interface-database.cc mv -f .deps/c-interface-database.Tpo .deps/c-interface-database.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-pisa.o -MD -MP -MF .deps/c-interface-pisa.Tpo -c -o c-interface-pisa.o c-interface-pisa.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-pisa.cc:22: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from graphics-info.h:31, from c-interface-pisa.cc:22: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-pisa.cc:22: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from graphics-info.h:31, from c-interface-pisa.cc:22: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-pisa.Tpo .deps/c-interface-pisa.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface.o -MD -MP -MF .deps/c-interface.Tpo -c -o c-interface.o c-interface.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface-python.hh:29, from c-interface.cc:52: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface.cc:28: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface-python.hh:29, from c-interface.cc:52: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface.cc:28: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface.Tpo .deps/c-interface.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-gui.o -MD -MP -MF .deps/c-interface-gui.Tpo -c -o c-interface-gui.o c-interface-gui.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-gui.cc:61: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from c-interface-gui.cc:27: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-gui.cc:61: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from c-interface-gui.cc:27: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-gui.Tpo .deps/c-interface-gui.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-gtk2.o -MD -MP -MF .deps/c-interface-gtk2.Tpo -c -o c-interface-gtk2.o c-interface-gtk2.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from c-interface-gtk2.cc:57: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/sys/types.h:27, from c-interface-gtk2.cc:23: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from c-interface-gtk2.cc:57: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/sys/types.h:27, from c-interface-gtk2.cc:23: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-gtk2.Tpo .deps/c-interface-gtk2.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-info.o -MD -MP -MF .deps/c-interface-info.Tpo -c -o c-interface-info.o c-interface-info.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-info.cc:66: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-info.cc:28: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-info.cc:66: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-info.cc:28: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-info.Tpo .deps/c-interface-info.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-ligands.o -MD -MP -MF .deps/c-interface-ligands.Tpo -c -o c-interface-ligands.o c-interface-ligands.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-ligands.cc:44: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-ligands.cc:21: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-ligands.cc:44: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-ligands.cc:21: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-ligands.Tpo .deps/c-interface-ligands.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-ligands-gui.o -MD -MP -MF .deps/c-interface-ligands-gui.Tpo -c -o c-interface-ligands-gui.o c-interface-ligands-gui.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-ligands-gui.cc:44: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-ligands-gui.cc:21: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-ligands-gui.cc:44: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-ligands-gui.cc:21: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-ligands-gui.Tpo .deps/c-interface-ligands-gui.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-mmdb.o -MD -MP -MF .deps/c-interface-mmdb.Tpo -c -o c-interface-mmdb.o c-interface-mmdb.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface-mmdb.hh:42, from c-interface-mmdb.cc:32: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from c-interface-mmdb.cc:26: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface-mmdb.hh:42, from c-interface-mmdb.cc:32: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from c-interface-mmdb.cc:26: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-mmdb.Tpo .deps/c-interface-mmdb.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-mutate.o -MD -MP -MF .deps/c-interface-mutate.Tpo -c -o c-interface-mutate.o c-interface-mutate.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-mutate.cc:40: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-mutate.cc:24: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-mutate.cc:40: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-mutate.cc:24: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-mutate.Tpo .deps/c-interface-mutate.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-ncs.o -MD -MP -MF .deps/c-interface-ncs.Tpo -c -o c-interface-ncs.o c-interface-ncs.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-ncs.cc:49: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-ncs.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-ncs.cc:49: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-ncs.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-ncs.Tpo .deps/c-interface-ncs.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-nucleotides.o -MD -MP -MF .deps/c-interface-nucleotides.Tpo -c -o c-interface-nucleotides.o c-interface-nucleotides.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-nucleotides.cc:30: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from c-interface-nucleotides.cc:22: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-nucleotides.cc:30: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from c-interface-nucleotides.cc:22: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-nucleotides.Tpo .deps/c-interface-nucleotides.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-python.o -MD -MP -MF .deps/c-interface-python.Tpo -c -o c-interface-python.o c-interface-python.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface-python.hh:29, from c-interface-python.cc:28: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from c-interface-python.cc:22: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface-python.hh:29, from c-interface-python.cc:28: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from c-interface-python.cc:22: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-python.Tpo .deps/c-interface-python.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-preferences.o -MD -MP -MF .deps/c-interface-preferences.Tpo -c -o c-interface-preferences.o c-interface-preferences.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-preferences.cc:52: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from c-interface-preferences.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-preferences.cc:52: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from c-interface-preferences.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-preferences.Tpo .deps/c-interface-preferences.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-scm.o -MD -MP -MF .deps/c-interface-scm.Tpo -c -o c-interface-scm.o c-interface-scm.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-scm.cc:28: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from c-interface-scm.cc:22: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-scm.cc:28: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from c-interface-scm.cc:22: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-scm.Tpo .deps/c-interface-scm.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-superpose.o -MD -MP -MF .deps/c-interface-superpose.Tpo -c -o c-interface-superpose.o c-interface-superpose.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-superpose.cc:31: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from graphics-info.h:31, from c-interface-superpose.cc:31: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-superpose.cc:31: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from graphics-info.h:31, from c-interface-superpose.cc:31: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-superpose.Tpo .deps/c-interface-superpose.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-validate.o -MD -MP -MF .deps/c-interface-validate.Tpo -c -o c-interface-validate.o c-interface-validate.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-validate.cc:48: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-validate.cc:27: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-validate.cc:48: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-validate.cc:27: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-validate.Tpo .deps/c-interface-validate.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-widgets.o -MD -MP -MF .deps/c-interface-widgets.Tpo -c -o c-interface-widgets.o c-interface-widgets.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-widgets.cc:28: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from c-interface-widgets.cc:24: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-widgets.cc:28: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from c-interface-widgets.cc:24: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-widgets.Tpo .deps/c-interface-widgets.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT c-interface-waters.o -MD -MP -MF .deps/c-interface-waters.Tpo -c -o c-interface-waters.o c-interface-waters.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-waters.cc:49: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-waters.cc:24: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from c-interface-waters.cc:49: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from c-interface-waters.cc:24: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/c-interface-waters.Tpo .deps/c-interface-waters.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT callbacks.o -MD -MP -MF .deps/callbacks.Tpo -c -o callbacks.o callbacks.c mv -f .deps/callbacks.Tpo .deps/callbacks.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT cmtz-interface.o -MD -MP -MF .deps/cmtz-interface.Tpo -c -o cmtz-interface.o cmtz-interface.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from cmtz-interface.cc:53: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from cmtz-interface.cc:22: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from cmtz-interface.cc:53: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from cmtz-interface.cc:22: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/cmtz-interface.Tpo .deps/cmtz-interface.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT command-line.o -MD -MP -MF .deps/command-line.Tpo -c -o command-line.o command-line.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from command-line.cc:49: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/unistd.h:26, from command-line.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from command-line.cc:49: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/unistd.h:26, from command-line.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/command-line.Tpo .deps/command-line.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-align.o -MD -MP -MF .deps/coot-align.Tpo -c -o coot-align.o coot-align.cc mv -f .deps/coot-align.Tpo .deps/coot-align.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-nomenclature.o -MD -MP -MF .deps/coot-nomenclature.Tpo -c -o coot-nomenclature.o coot-nomenclature.cc mv -f .deps/coot-nomenclature.Tpo .deps/coot-nomenclature.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-glue.o -MD -MP -MF .deps/coot-glue.Tpo -c -o coot-glue.o coot-glue.c mv -f .deps/coot-glue.Tpo .deps/coot-glue.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-glue-gtk2.o -MD -MP -MF .deps/coot-glue-gtk2.Tpo -c -o coot-glue-gtk2.o coot-glue-gtk2.c mv -f .deps/coot-glue-gtk2.Tpo .deps/coot-glue-gtk2.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot-glue-gtk2-python.o -MD -MP -MF .deps/coot-glue-gtk2-python.Tpo -c -o coot-glue-gtk2-python.o coot-glue-gtk2-python.cc mv -f .deps/coot-glue-gtk2-python.Tpo .deps/coot-glue-gtk2-python.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot_pythonmodule.o -MD -MP -MF .deps/coot_pythonmodule.Tpo -c -o coot_pythonmodule.o coot_pythonmodule.cc In file included from /usr/include/python2.6/Python.h:8, from /usr/include/pygtk-2.0/pygobject.h:5, from coot_pythonmodule.cc:28: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/limits.h:27, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:122, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/syslimits.h:7, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:11, from /usr/lib/glib-2.0/include/glibconfig.h:11, from /usr/include/glib-2.0/glib/gtypes.h:34, from /usr/include/glib-2.0/glib/galloca.h:34, from /usr/include/glib-2.0/glib.h:32, from /usr/include/glib-2.0/gobject/gtype.h:26, from /usr/include/glib-2.0/gobject/gboxed.h:26, from /usr/include/glib-2.0/glib-object.h:25, from /usr/include/glib-2.0/gio/gioenums.h:30, from /usr/include/glib-2.0/gio/giotypes.h:30, from /usr/include/glib-2.0/gio/gio.h:28, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:32, from coot_pythonmodule.cc:24: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from /usr/include/pygtk-2.0/pygobject.h:5, from coot_pythonmodule.cc:28: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/limits.h:27, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:122, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/syslimits.h:7, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:11, from /usr/lib/glib-2.0/include/glibconfig.h:11, from /usr/include/glib-2.0/glib/gtypes.h:34, from /usr/include/glib-2.0/glib/galloca.h:34, from /usr/include/glib-2.0/glib.h:32, from /usr/include/glib-2.0/gobject/gtype.h:26, from /usr/include/glib-2.0/gobject/gboxed.h:26, from /usr/include/glib-2.0/glib-object.h:25, from /usr/include/glib-2.0/gio/gioenums.h:30, from /usr/include/glib-2.0/gio/giotypes.h:30, from /usr/include/glib-2.0/gio/gio.h:28, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:32, from coot_pythonmodule.cc:24: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/coot_pythonmodule.Tpo .deps/coot_pythonmodule.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT geometry-graphs.o -MD -MP -MF .deps/geometry-graphs.Tpo -c -o geometry-graphs.o geometry-graphs.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from geometry-graphs.cc:72: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from ../coot-utils/coot-coord-utils.hh:28, from geometry-graphs.cc:23: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from geometry-graphs.cc:72: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from ../coot-utils/coot-coord-utils.hh:28, from geometry-graphs.cc:23: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/geometry-graphs.Tpo .deps/geometry-graphs.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT get-residue.o -MD -MP -MF .deps/get-residue.Tpo -c -o get-residue.o get-residue.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from get-residue.cc:3: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from graphics-info.h:31, from get-residue.cc:3: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from get-residue.cc:3: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from graphics-info.h:31, from get-residue.cc:3: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/get-residue.Tpo .deps/get-residue.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT globjects.o -MD -MP -MF .deps/globjects.Tpo -c -o globjects.o globjects.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from globjects.cc:67: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/limits.h:27, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:122, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/syslimits.h:7, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:11, from /usr/lib/glib-2.0/include/glibconfig.h:11, from /usr/include/glib-2.0/glib/gtypes.h:34, from /usr/include/glib-2.0/glib/galloca.h:34, from /usr/include/glib-2.0/glib.h:32, from /usr/include/glib-2.0/gobject/gtype.h:26, from /usr/include/glib-2.0/gobject/gboxed.h:26, from /usr/include/glib-2.0/glib-object.h:25, from /usr/include/glib-2.0/gio/gioenums.h:30, from /usr/include/glib-2.0/gio/giotypes.h:30, from /usr/include/glib-2.0/gio/gio.h:28, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:32, from globjects.cc:33: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from globjects.cc:67: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/limits.h:27, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:122, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/syslimits.h:7, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:11, from /usr/lib/glib-2.0/include/glibconfig.h:11, from /usr/include/glib-2.0/glib/gtypes.h:34, from /usr/include/glib-2.0/glib/galloca.h:34, from /usr/include/glib-2.0/glib.h:32, from /usr/include/glib-2.0/gobject/gtype.h:26, from /usr/include/glib-2.0/gobject/gboxed.h:26, from /usr/include/glib-2.0/glib-object.h:25, from /usr/include/glib-2.0/gio/gioenums.h:30, from /usr/include/glib-2.0/gio/giotypes.h:30, from /usr/include/glib-2.0/gio/gio.h:28, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:32, from globjects.cc:33: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/globjects.Tpo .deps/globjects.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info.o -MD -MP -MF .deps/graphics-info.Tpo -c -o graphics-info.o graphics-info.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info.cc:73: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info.cc:73: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info.Tpo .deps/graphics-info.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-defines.o -MD -MP -MF .deps/graphics-info-defines.Tpo -c -o graphics-info-defines.o graphics-info-defines.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-defines.cc:27: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from graphics-info.h:31, from graphics-info-defines.cc:27: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-defines.cc:27: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from graphics-info.h:31, from graphics-info-defines.cc:27: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-defines.Tpo .deps/graphics-info-defines.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-refmac.o -MD -MP -MF .deps/graphics-info-refmac.Tpo -c -o graphics-info-refmac.o graphics-info-refmac.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-refmac.cc:81: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-refmac.cc:33: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-refmac.cc:81: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-refmac.cc:33: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-refmac.Tpo .deps/graphics-info-refmac.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-graphs.o -MD -MP -MF .deps/graphics-info-graphs.Tpo -c -o graphics-info-graphs.o graphics-info-graphs.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-graphs.cc:72: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-graphs.cc:26: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-graphs.cc:72: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-graphs.cc:26: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-graphs.Tpo .deps/graphics-info-graphs.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-gui.o -MD -MP -MF .deps/graphics-info-gui.Tpo -c -o graphics-info-gui.o graphics-info-gui.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-gui.cc:73: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-gui.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-gui.cc:73: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-gui.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-gui.Tpo .deps/graphics-info-gui.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-modelling.o -MD -MP -MF .deps/graphics-info-modelling.Tpo -c -o graphics-info-modelling.o graphics-info-modelling.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-modelling.cc:80: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-modelling.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-modelling.cc:80: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-modelling.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-modelling.Tpo .deps/graphics-info-modelling.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-navigation.o -MD -MP -MF .deps/graphics-info-navigation.Tpo -c -o graphics-info-navigation.o graphics-info-navigation.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-navigation.cc:52: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-navigation.cc:31: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-navigation.cc:52: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-navigation.cc:31: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-navigation.Tpo .deps/graphics-info-navigation.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-navigation-gtk1.o -MD -MP -MF .deps/graphics-info-navigation-gtk1.Tpo -c -o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk1.cc mv -f .deps/graphics-info-navigation-gtk1.Tpo .deps/graphics-info-navigation-gtk1.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-navigation-gtk2.o -MD -MP -MF .deps/graphics-info-navigation-gtk2.Tpo -c -o graphics-info-navigation-gtk2.o graphics-info-navigation-gtk2.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-navigation-gtk2.cc:40: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/limits.h:27, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:122, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/syslimits.h:7, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:11, from /usr/lib/glib-2.0/include/glibconfig.h:11, from /usr/include/glib-2.0/glib/gtypes.h:34, from /usr/include/glib-2.0/glib/galloca.h:34, from /usr/include/glib-2.0/glib.h:32, from /usr/include/glib-2.0/gobject/gtype.h:26, from /usr/include/glib-2.0/gobject/gboxed.h:26, from /usr/include/glib-2.0/glib-object.h:25, from /usr/include/glib-2.0/gio/gioenums.h:30, from /usr/include/glib-2.0/gio/giotypes.h:30, from /usr/include/glib-2.0/gio/gio.h:28, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:32, from graphics-info-navigation-gtk2.cc:22: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-navigation-gtk2.cc:40: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/limits.h:27, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:122, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/syslimits.h:7, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include-fixed/limits.h:11, from /usr/lib/glib-2.0/include/glibconfig.h:11, from /usr/include/glib-2.0/glib/gtypes.h:34, from /usr/include/glib-2.0/glib/galloca.h:34, from /usr/include/glib-2.0/glib.h:32, from /usr/include/glib-2.0/gobject/gtype.h:26, from /usr/include/glib-2.0/gobject/gboxed.h:26, from /usr/include/glib-2.0/glib-object.h:25, from /usr/include/glib-2.0/gio/gioenums.h:30, from /usr/include/glib-2.0/gio/giotypes.h:30, from /usr/include/glib-2.0/gio/gio.h:28, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:32, from graphics-info-navigation-gtk2.cc:22: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-navigation-gtk2.Tpo .deps/graphics-info-navigation-gtk2.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-preferences.o -MD -MP -MF .deps/graphics-info-preferences.Tpo -c -o graphics-info-preferences.o graphics-info-preferences.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-preferences.cc:28: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iosfwd:40, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ios:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/istream:40, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/fstream:40, from graphics-info-preferences.cc:24: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-preferences.cc:28: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iosfwd:40, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ios:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/istream:40, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/fstream:40, from graphics-info-preferences.cc:24: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-preferences.Tpo .deps/graphics-info-preferences.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-mutate.o -MD -MP -MF .deps/graphics-info-mutate.Tpo -c -o graphics-info-mutate.o graphics-info-mutate.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-mutate.cc:63: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/sys/types.h:27, from graphics-info-mutate.cc:23: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-mutate.cc:63: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/sys/types.h:27, from graphics-info-mutate.cc:23: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-mutate.Tpo .deps/graphics-info-mutate.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-lsq.o -MD -MP -MF .deps/graphics-info-lsq.Tpo -c -o graphics-info-lsq.o graphics-info-lsq.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-lsq.cc:49: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-lsq.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-lsq.cc:49: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-lsq.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-lsq.Tpo .deps/graphics-info-lsq.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-pick.o -MD -MP -MF .deps/graphics-info-pick.Tpo -c -o graphics-info-pick.o graphics-info-pick.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-pick.cc:38: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-pick.cc:21: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-pick.cc:38: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from graphics-info-pick.cc:21: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-pick.Tpo .deps/graphics-info-pick.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-render.o -MD -MP -MF .deps/graphics-info-render.Tpo -c -o graphics-info-render.o graphics-info-render.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-render.cc:32: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from graphics-info-render.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-render.cc:32: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from graphics-info-render.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-render.Tpo .deps/graphics-info-render.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-state.o -MD -MP -MF .deps/graphics-info-state.Tpo -c -o graphics-info-state.o graphics-info-state.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-state.cc:30: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iosfwd:40, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ios:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/istream:40, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/fstream:40, from graphics-info-state.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-state.cc:30: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iosfwd:40, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/ios:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/istream:40, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/fstream:40, from graphics-info-state.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-state.Tpo .deps/graphics-info-state.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT graphics-info-superpose.o -MD -MP -MF .deps/graphics-info-superpose.Tpo -c -o graphics-info-superpose.o graphics-info-superpose.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-superpose.cc:26: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from graphics-info-superpose.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from graphics-info-superpose.cc:26: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from graphics-info-superpose.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/graphics-info-superpose.Tpo .deps/graphics-info-superpose.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT gl-matrix.o -MD -MP -MF .deps/gl-matrix.Tpo -c -o gl-matrix.o gl-matrix.cc mv -f .deps/gl-matrix.Tpo .deps/gl-matrix.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT gtk-manual.o -MD -MP -MF .deps/gtk-manual.Tpo -c -o gtk-manual.o gtk-manual.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from gtk-manual.cc:32: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/string.h:26, from gtk-manual.cc:28: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from gtk-manual.cc:32: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/string.h:26, from gtk-manual.cc:28: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/gtk-manual.Tpo .deps/gtk-manual.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT gtk2-interface.o -MD -MP -MF .deps/gtk2-interface.Tpo -c -o gtk2-interface.o gtk2-interface.c mv -f .deps/gtk2-interface.Tpo .deps/gtk2-interface.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c mv -f .deps/interface.Tpo .deps/interface.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT molecule-class-info.o -MD -MP -MF .deps/molecule-class-info.Tpo -c -o molecule-class-info.o molecule-class-info.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info.cc:69: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from molecule-class-info.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info.cc:69: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from molecule-class-info.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/molecule-class-info.Tpo .deps/molecule-class-info.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT molecule-class-info-maps.o -MD -MP -MF .deps/molecule-class-info-maps.Tpo -c -o molecule-class-info-maps.o molecule-class-info-maps.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-maps.cc:63: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/sys/types.h:27, from molecule-class-info-maps.cc:31: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-maps.cc:63: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/sys/types.h:27, from molecule-class-info-maps.cc:31: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/molecule-class-info-maps.Tpo .deps/molecule-class-info-maps.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT molecule-class-info-other.o -MD -MP -MF .deps/molecule-class-info-other.Tpo -c -o molecule-class-info-other.o molecule-class-info-other.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-other.cc:64: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from molecule-class-info-other.cc:24: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-other.cc:64: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from molecule-class-info-other.cc:24: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/molecule-class-info-other.Tpo .deps/molecule-class-info-other.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT molecule-class-info-mutate.o -MD -MP -MF .deps/molecule-class-info-mutate.Tpo -c -o molecule-class-info-mutate.o molecule-class-info-mutate.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-mutate.cc:44: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from molecule-class-info-mutate.cc:28: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-mutate.cc:44: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from molecule-class-info-mutate.cc:28: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/molecule-class-info-mutate.Tpo .deps/molecule-class-info-mutate.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT molecule-class-info-residues.o -MD -MP -MF .deps/molecule-class-info-residues.Tpo -c -o molecule-class-info-residues.o molecule-class-info-residues.cc mv -f .deps/molecule-class-info-residues.Tpo .deps/molecule-class-info-residues.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT molecule-class-info-surface.o -MD -MP -MF .deps/molecule-class-info-surface.Tpo -c -o molecule-class-info-surface.o molecule-class-info-surface.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-surface.cc:33: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from molecule-class-info-surface.cc:25: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-surface.cc:33: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from molecule-class-info-surface.cc:25: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/molecule-class-info-surface.Tpo .deps/molecule-class-info-surface.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT molecule-class-info-ncs.o -MD -MP -MF .deps/molecule-class-info-ncs.Tpo -c -o molecule-class-info-ncs.o molecule-class-info-ncs.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-ncs.cc:42: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/exception:37, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/stdexcept:38, from molecule-class-info-ncs.cc:29: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from molecule-class-info-ncs.cc:42: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/exception:37, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/stdexcept:38, from molecule-class-info-ncs.cc:29: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/molecule-class-info-ncs.Tpo .deps/molecule-class-info-ncs.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT molecule-class-info-widget-work.o -MD -MP -MF .deps/molecule-class-info-widget-work.Tpo -c -o molecule-class-info-widget-work.o molecule-class-info-widget-work.cc mv -f .deps/molecule-class-info-widget-work.Tpo .deps/molecule-class-info-widget-work.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT nsv.o -MD -MP -MF .deps/nsv.Tpo -c -o nsv.o nsv.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from nsv.cc:38: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from nsv.cc:29: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from nsv.cc:38: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from nsv.cc:29: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/nsv.Tpo .deps/nsv.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT pick.o -MD -MP -MF .deps/pick.Tpo -c -o pick.o pick.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from pick.cc:40: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from pick.cc:22: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from pick.cc:40: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/string:40, from pick.cc:22: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/pick.Tpo .deps/pick.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT read-phs.o -MD -MP -MF .deps/read-phs.Tpo -c -o read-phs.o read-phs.c mv -f .deps/read-phs.Tpo .deps/read-phs.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT read-cif.o -MD -MP -MF .deps/read-cif.Tpo -c -o read-cif.o read-cif.c mv -f .deps/read-cif.Tpo .deps/read-cif.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT rama_mousey.o -MD -MP -MF .deps/rama_mousey.Tpo -c -o rama_mousey.o rama_mousey.cc mv -f .deps/rama_mousey.Tpo .deps/rama_mousey.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT rama_plot.o -MD -MP -MF .deps/rama_plot.Tpo -c -o rama_plot.o rama_plot.cc In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from rama_plot.cc:79: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from rama_plot.cc:33: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from rama_plot.cc:79: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/iostream:39, from rama_plot.cc:33: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/rama_plot.Tpo .deps/rama_plot.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT restraints-editor.o -MD -MP -MF .deps/restraints-editor.Tpo -c -o restraints-editor.o restraints-editor.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from restraints-editor.cc:46: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from restraints-editor.cc:22: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from restraints-editor.cc:46: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:243, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/bits/stl_algobase.h:60, from /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/include/g++-v4/vector:61, from restraints-editor.cc:22: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/restraints-editor.Tpo .deps/restraints-editor.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT support.o -MD -MP -MF .deps/support.Tpo -c -o support.o support.c mv -f .deps/support.Tpo .deps/support.Po i686-pc-linux-gnu-gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 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-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT fix-nomenclature.o -MD -MP -MF .deps/fix-nomenclature.Tpo -c -o fix-nomenclature.o fix-nomenclature.cc mv -f .deps/fix-nomenclature.Tpo .deps/fix-nomenclature.Po /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-wrap-python.la -rpath /usr/lib coot_wrap_python.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/coot_wrap_python.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -pthread -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -pthread -Wl,-soname -Wl,libcoot-wrap-python.so.0 -o .libs/libcoot-wrap-python.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-wrap-python.so.0" && ln -s "libcoot-wrap-python.so.0.0.0" "libcoot-wrap-python.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-wrap-python.so" && ln -s "libcoot-wrap-python.so.0.0.0" "libcoot-wrap-python.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-wrap-python.a coot_wrap_python.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-wrap-python.a libtool: link: ( cd ".libs" && rm -f "libcoot-wrap-python.la" && ln -s "../libcoot-wrap-python.la" "libcoot-wrap-python.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o density-score-by-residue-real density-score-by-residue.o ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-utils.la ../compat/libcoot-compat.la -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/density-score-by-residue-real density-score-by-residue.o ../geometry/.libs/libcoot-geometry.so -L/usr/lib -L/usr ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so ../coot-utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so -lz /usr/lib/libmmdb.so /usr/lib/libgsl.so -L/usr/lib/blas/threaded-atlas /usr/lib/blas/threaded-atlas/libcblas.so -lcblas /usr/lib/libatlas.so -lpthread -lm -pthread -Wl,-rpath -Wl,/usr/lib/blas/threaded-atlas /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/libcoot-ligand.la ../db-main/libcoot-db-main.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-utils.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -L/usr -lmmdb -lm libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer 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../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol/.libs/libcoot-mini-mol.so ../ccp4mg-utils/.libs/libccp4mg-utils.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-utils.so ../coot-utils/.libs/libcoot-shelx.so ../mini-mol/.libs/libcoot-mini-mol.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so /usr/lib/libgsl.so /usr/lib/blas/threaded-atlas/libcblas.so -lcblas /usr/lib/libatlas.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so 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-I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT svn-revision.o -MD -MP -MF .deps/svn-revision.Tpo -c -o svn-revision.o svn-revision.cc mv -f .deps/svn-revision.Tpo .deps/svn-revision.Po i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cc In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from main.cc:96: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/sys/time.h:23, from main.cc:29: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from graphics-info.h:88, from main.cc:96: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/sys/time.h:23, from main.cc:29: /usr/include/features.h:160:1: warning: this is the location of the previous definition mv -f .deps/main.Tpo .deps/main.Po /bin/sh ../libtool --tag=CXX --mode=compile i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot_wrap_guile.lo -MD -MP -MF .deps/coot_wrap_guile.Tpo -c -o coot_wrap_guile.lo coot_wrap_guile.cc libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot_wrap_guile.lo -MD -MP -MF .deps/coot_wrap_guile.Tpo -c coot_wrap_guile.cc -fPIC -DPIC -o .libs/coot_wrap_guile.o In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from coot_wrap_guile.cc:1305: /usr/include/python2.6/pyconfig.h:1052:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/string.h:26, from coot_wrap_guile.cc:330: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/Python.h:8, from c-interface.h:71, from coot_wrap_guile.cc:1305: /usr/include/python2.6/pyconfig.h:1064:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/string.h:26, from coot_wrap_guile.cc:330: /usr/include/features.h:160:1: warning: this is the location of the previous definition libtool: compile: i686-pc-linux-gnu-g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.6-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -I../compat -I../coords -I../ccp4mg-utils -I../coot-utils -I../intl -I../skeleton -I../angles -I../atom-utils -I../db-main -I../mini-mol -I../ligand -I../sequence-view -I../geometry -I../ideal -I../coot-surface -I../surface -I../density-contour -I../build -I../high-res -I../analysis -I../cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/pango-1.0 -I/usr/include/gail-1.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/freetype2 -I/usr/include/atk-1.0 -I/usr/lib/gtk-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/libpng12 -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/atk-1.0 -I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -DHAVE_SSMLIB -I/usr/include/ssm -I/usr/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/usr/include -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -MT coot_wrap_guile.lo -MD -MP -MF .deps/coot_wrap_guile.Tpo -c coot_wrap_guile.cc -o coot_wrap_guile.o >/dev/null 2>&1 mv -f .deps/coot_wrap_guile.Tpo .deps/coot_wrap_guile.Plo /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o libcoot-wrap-guile.la -rpath /usr/lib coot_wrap_guile.lo libtool: link: i686-pc-linux-gnu-g++ -shared -nostdlib /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crti.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtbeginS.o .libs/coot_wrap_guile.o -L/opt/intel/Compiler/11.1/046/lib/ia32 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1 -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/crtendS.o /usr/lib/gcc/i686-pc-linux-gnu/4.4.1/../../../crtn.o -pthread -march=prescott -mmmx -msse2 -mcx16 -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -pthread -Wl,-soname -Wl,libcoot-wrap-guile.so.0 -o .libs/libcoot-wrap-guile.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-wrap-guile.so.0" && ln -s "libcoot-wrap-guile.so.0.0.0" "libcoot-wrap-guile.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-wrap-guile.so" && ln -s "libcoot-wrap-guile.so.0.0.0" "libcoot-wrap-guile.so") libtool: link: i686-pc-linux-gnu-ar cru .libs/libcoot-wrap-guile.a coot_wrap_guile.o libtool: link: i686-pc-linux-gnu-ranlib .libs/libcoot-wrap-guile.a libtool: link: ( cd ".libs" && rm -f "libcoot-wrap-guile.la" && ln -s "../libcoot-wrap-guile.la" "libcoot-wrap-guile.la" ) /bin/sh ../libtool --tag=CXX --mode=link i686-pc-linux-gnu-g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-GenuineIntel---python-gtk2"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -o coot-real main.o svn-revision.o c-inner-main.o c-interface-build.o c-interface-build-gui.o c-interface-database.o c-interface-pisa.o c-interface.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-mmdb.o c-interface-mutate.o c-interface-ncs.o c-interface-nucleotides.o c-interface-python.o c-interface-preferences.o c-interface-scm.o c-interface-superpose.o c-interface-validate.o c-interface-widgets.o c-interface-waters.o callbacks.o cmtz-interface.o command-line.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot_pythonmodule.o geometry-graphs.o get-residue.o globjects.o graphics-info.o graphics-info-defines.o graphics-info-refmac.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-render.o graphics-info-state.o graphics-info-superpose.o gl-matrix.o gtk-manual.o gtk2-interface.o interface.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-other.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o support.o support-gtk2-extras.o testing.o trackball.o xmap-utils.o ../ligand/libcoot-ligand.la ../density-contour/libcoot-isosurface.la ../build/libcoot-cabuild.la ../skeleton/libcoot-skeleton.la ../angles/libcoot-AngleInfo.la ../atom-utils/libcoot-atomutils.la ../db-main/libcoot-db-main.la ../sequence-view/libcoot-sequence-view.la ../high-res/libcoot-high-res.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-surface/libcoot-surface.la ../surface/libccp4mg-surface.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-heavy.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../analysis/libcoot-analysis.la ../cootaneer/libcootaneer.la ../compat/libcoot-compat.la libcoot-wrap-guile.la libcoot-wrap-python.la -lguilegtk-2.0 -pthread -lguile -lltdl -Wl,-O1,--hash-style=gnu,--sort-common,--as-needed -lgmp -lcrypt -lm -lltdl -L/usr/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/usr/lib -L/usr -lmmdb -lm -lsrfftw -lsfftw -lz -lm -lpthread -L/usr/lib -lssm -L/usr/lib -L/usr -lmmdb -lm -L/usr/lib/python2.6/config -lpython2.6 -lutil -Wl,--export-dynamic -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE -lgtk-x11-2.0 -lpangox-1.0 -lX11 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lgnomecanvas-2 -lart_lgpl_2 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -L/usr/lib -lgsl -L/usr/lib/blas/threaded-atlas -lcblas -latlas -lm -lglade-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 libtool: link: i686-pc-linux-gnu-g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-GenuineIntel---python-gtk2\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -pthread -DUSE_PYTHON -I/usr/include/python2.6 -DUSE_PYGTK -DHAVE_GSL -O2 -pipe -march=prescott -fomit-frame-pointer -mmmx -msse2 -mcx16 -frecord-gcc-switches -floop-interchange -floop-strip-mine -floop-block -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -o .libs/coot-real main.o svn-revision.o c-inner-main.o c-interface-build.o c-interface-build-gui.o c-interface-database.o c-interface-pisa.o c-interface.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-mmdb.o c-interface-mutate.o c-interface-ncs.o c-interface-nucleotides.o c-interface-python.o c-interface-preferences.o c-interface-scm.o c-interface-superpose.o c-interface-validate.o c-interface-widgets.o c-interface-waters.o callbacks.o cmtz-interface.o command-line.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot_pythonmodule.o geometry-graphs.o get-residue.o globjects.o graphics-info.o graphics-info-defines.o graphics-info-refmac.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-render.o graphics-info-state.o graphics-info-superpose.o gl-matrix.o gtk-manual.o gtk2-interface.o interface.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-other.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o support.o support-gtk2-extras.o testing.o trackball.o xmap-utils.o -pthread -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,--as-needed -Wl,--export-dynamic ../ligand/.libs/libcoot-ligand.so -L/usr/lib -L/usr/lib/blas/threaded-atlas -L/usr ../density-contour/.libs/libcoot-isosurface.so ../build/.libs/libcoot-cabuild.so ../skeleton/.libs/libcoot-skeleton.so /var/tmp/portage/sci-chemistry/coot-9999/work/atom-utils/.libs/libcoot-atomutils.so ../angles/.libs/libcoot-AngleInfo.so ../atom-utils/.libs/libcoot-atomutils.so ../db-main/.libs/libcoot-db-main.so ../sequence-view/.libs/libcoot-sequence-view.so ../high-res/.libs/libcoot-high-res.so /var/tmp/portage/sci-chemistry/coot-9999/work/ligand/.libs/libcoot-ligand.so /var/tmp/portage/sci-chemistry/coot-9999/work/ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-9999/work/coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-9999/work/db-main/.libs/libcoot-db-main.so /var/tmp/portage/sci-chemistry/coot-9999/work/geometry/.libs/libcoot-geometry.so /var/tmp/portage/sci-chemistry/coot-9999/work/ccp4mg-utils/.libs/libccp4mg-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-map-utils.so ../ideal/.libs/libcoot-ideal.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-shelx.so /var/tmp/portage/sci-chemistry/coot-9999/work/mini-mol/.libs/libcoot-mini-mol.so ../coot-surface/.libs/libcoot-surface.so /var/tmp/portage/sci-chemistry/coot-9999/work/surface/.libs/libccp4mg-surface.so ../surface/.libs/libccp4mg-surface.so ../ccp4mg-utils/.libs/libccp4mg-utils.so ../coot-utils/.libs/libcoot-map-heavy.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../analysis/.libs/libcoot-analysis.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-coord-utils.so /var/tmp/portage/sci-chemistry/coot-9999/work/coot-utils/.libs/libcoot-utils.so ../cootaneer/.libs/libcootaneer.so ../compat/.libs/libcoot-compat.so ./.libs/libcoot-wrap-guile.so ./.libs/libcoot-wrap-python.so /usr/lib/libguilegtk-2.0.so /usr/lib/libgthread-2.0.so -lrt /usr/lib/libguile.so /usr/lib/libgmp.so -lcrypt /usr/lib/libltdl.so /usr/lib/libclipper-ccp4.so /usr/lib/libclipper-cif.so /usr/lib/libclipper-phs.so /usr/lib/libclipper-contrib.so /usr/lib/libclipper-minimol.so /usr/lib/libclipper-cns.so /usr/lib/libclipper-mmdb.so /usr/lib/libclipper-core.so -lccp4c /usr/lib/libsrfftw.so /usr/lib/libsfftw.so /usr/lib/libssm.so -L/var/tmp/portage/sci-libs/ccp4-libs-6.1.2/work/ccp4-6.1.2/lib/src /usr/lib/libmmdb.so -L/usr/lib/python2.6/config -lpython2.6 -lutil /usr/lib/libgtkglext-x11-1.0.so /usr/lib/libgdkglext-x11-1.0.so /usr/lib/libpangox-1.0.so /usr/lib/libglut.so /usr/lib/libGLU.so /usr/lib/libGL.so -lstdc++ /usr/lib/libXxf86vm.so /usr/lib/libXmu.so /usr/lib/libXt.so /usr/lib/libSM.so /usr/lib/libICE.so -luuid /usr/lib/libgnomecanvas-2.so /usr/lib/libgailutil.so /usr/lib/libXi.so /usr/lib/libXrandr.so /usr/lib/libXcursor.so /usr/lib/libXcomposite.so /usr/lib/libXext.so /usr/lib/libXdamage.so /usr/lib/libXfixes.so /usr/lib/libart_lgpl_2.so /usr/lib/libgsl.so /usr/lib/blas/threaded-atlas/libcblas.so -lcblas /usr/lib/libatlas.so -lpthread /usr/lib/libglade-2.0.so /usr/lib/libxml2.so /usr/lib/libgtk-x11-2.0.so /usr/lib/libgdk-x11-2.0.so /usr/lib/libatk-1.0.so /usr/lib/libgdk_pixbuf-2.0.so /usr/lib/libgio-2.0.so /usr/lib/libpangocairo-1.0.so /usr/lib/libpangoft2-1.0.so /usr/lib/libcairo.so /usr/lib/libpixman-1.so /usr/lib/libpng12.so /usr/lib/libXrender.so /usr/lib/libX11.so /usr/lib/libxcb.so /usr/lib/libXau.so /usr/lib/libXdmcp.so /usr/lib/libpango-1.0.so -lm /usr/lib/libfontconfig.so /usr/lib/libfreetype.so -lz /usr/lib/libexpat.so /usr/lib/libgobject-2.0.so /usr/lib/libgmodule-2.0.so -ldl /usr/lib/libglib-2.0.so -pthread -Wl,-rpath -Wl,/usr/lib/blas/threaded-atlas make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/src' Making all in rama-data make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/rama-data' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/rama-data' Making all in doc make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work/doc' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work/doc' make[1]: Entering directory `/var/tmp/portage/sci-chemistry/coot-9999/work' sed -e 's/#GTK2 //' ./cootrc.template > cootrc make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/coot-9999/work' >>> Source compiled. INFO:: splash_screen_pixmap_dir /var/tmp/portage/sci-chemistry/coot-9999/work/pixmaps INFO:: Colours file: /var/tmp/portage/sci-chemistry/coot-9999/work/colours.def loaded There are 118 data in /usr/share/ccp4//data/monomers/list/mon_lib_list.cif There are 2 data in /usr/share/ccp4//data/monomers/a/ALA.cif There are 2 data in /usr/share/ccp4//data/monomers/a/ASP.cif There are 2 data in /usr/share/ccp4//data/monomers/a/ASN.cif There are 2 data in /usr/share/ccp4//data/monomers/c/CYS.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GLN.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GLY.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GLU.cif There are 2 data in /usr/share/ccp4//data/monomers/p/PHE.cif There are 2 data in /usr/share/ccp4//data/monomers/h/HIS.cif There are 2 data in /usr/share/ccp4//data/monomers/i/ILE.cif There are 2 data in /usr/share/ccp4//data/monomers/l/LYS.cif There are 2 data in /usr/share/ccp4//data/monomers/l/LEU.cif There are 2 data in /usr/share/ccp4//data/monomers/m/MET.cif There are 2 data in /usr/share/ccp4//data/monomers/m/MSE.cif There are 2 data in /usr/share/ccp4//data/monomers/p/PRO.cif There are 2 data in /usr/share/ccp4//data/monomers/a/ARG.cif There are 2 data in /usr/share/ccp4//data/monomers/s/SER.cif There are 2 data in /usr/share/ccp4//data/monomers/t/THR.cif There are 2 data in /usr/share/ccp4//data/monomers/v/VAL.cif There are 2 data in /usr/share/ccp4//data/monomers/t/TRP.cif There are 2 data in /usr/share/ccp4//data/monomers/t/TYR.cif There are 2 data in /usr/share/ccp4//data/monomers/p/PO4.cif There are 2 data in /usr/share/ccp4//data/monomers/s/SO4.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GOL.cif There are 2 data in /usr/share/ccp4//data/monomers/e/ETH.cif There are 2 data in /usr/share/ccp4//data/monomers/c/CIT.cif There are 2 data in /usr/share/ccp4//data/monomers/a/AR.cif There are 2 data in /usr/share/ccp4//data/monomers/a/AD.cif There are 2 data in /usr/share/ccp4//data/monomers/c/CR.cif There are 2 data in /usr/share/ccp4//data/monomers/c/CD.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GR.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GD.cif There are 2 data in /usr/share/ccp4//data/monomers/t/TD.cif There are 2 data in /usr/share/ccp4//data/monomers/u/UR.cif Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/standard-residues.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) DEBUG:: stating pydirectory /var/tmp/portage/sci-chemistry/coot-9999/work/python INFO:: importing coot.py from /var/tmp/portage/sci-chemistry/coot-9999/work/python/coot.py Importing python module coot using command from coot import * INFO:: coot.py imported INFO loading coot python modules Running python script /var/tmp/portage/sci-chemistry/coot-9999/work/python/coot_load_modules.py Loading: coot_utils.py Loading: filter.py Loading: coot_lsq.py Loading: shelx.py Loading: get_ebi.py Loading: local_code.py Loading: hello.py Good Afternoon Justin, Welcome to Coot. (set-display-intro-string "Good Afternoon Justin, Welcome to Coot.") Loading: mutate.py Loading: refmac.py Loading: libcheck.py Loading: gap.py Loading: fitting.py Loading: raster3d.py Loading: povray.py Loading: remote_control.py Loading: generic_objects.py Loading: ncs.py Loading: cns2coot.py Loading: tips.py Loading: americanisms.py Loading: group_settings.py Loading: brute_lsqman.py INFO:: Creating directory /var/tmp/portage/sci-chemistry/coot-9999/work/.coot-preferences (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /var/tmp/portage/sci-chemistry/coot-9999/work/scheme/ load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" WARNING: (net http client): imported module (net http message) overrides core binding `version' load "local-code.scm" load "hello.scm" Good afternoon . Welcome to Coot. (set-display-intro-string "Good afternoon . Welcome to Coot") load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "parse-pisa-xml.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "americanisms.scm" load "group-settings.scm" (set-display-lists-for-maps 0) (filter-fileselection-filenames-state) (get-active-map-drag-flag) === greg-tests tests === Loading greg-tests/begin.grg ... =============================================================== ==================== Testing ================================== =============================================================== Loaded greg-tests/begin.grg Running 01-pdb+mtz.scm ... Entered testcase - Post Go To Atom no molecules (post-go-to-atom-window) Entered testcase - Close bad molecule (close-molecule -2) Entered testcase - Read coordinates test (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully Entered testcase - New molecule from bogus molecule Molecule number -5 is not a valid model molecule Entered testcase - New molecule from bogus atom selection in new_molecule_by_atom_selection Something bad happened - No atoms selected (info-dialog "Oops, failed to create fragment. No atoms selected Incorrect atom specifier? "//A/100"") INFO:: pre-n-molecules 1 post-n-molecules 1 Entered testcase - ins code change and Goto atom over an ins code break (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/ins-code-fragment-pre.pdb" 0) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/ins-code-fragment-pre.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 1 read successfully (set-go-to-atom-molecule 1) DEBUG:: Found chain_id A (change-residue-number 1 "A" 68 "" 68 "A") DEBUG:: Found chain_id A (change-residue-number 1 "A" 69 "" 68 "B") DEBUG:: Found chain_id A (change-residue-number 1 "A" 67 "" 68 "") pre and post ins codes: "" "A" pass: ("A" 68 "" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 70 "" " CA ") pass: ("A" 62 "" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "A" " CA ") pass: ("A" 68 "" " CA ") pass: ("A" 66 "" " CA ") Entered testcase - Read a bogus map WARNING:: Error reading bogus.map Read map bogus.map failed Entered testcase - Read MTZ test WARNING:: Can't find file bogus.mtz (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.09 seconds to read MTZ file INFO:: 0.064 seconds to initialize map INFO:: 0.093 seconds for FFT INFO:: 0.011 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.036 seconds for contour map INFO:: 0.294 seconds in total Entered testcase - Map Sigma INFO:: map sigmas 0.311501026153564 #f Entered testcase - Another Level Test making conventional map from MTZ filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.051 seconds to read MTZ file INFO:: 0.017 seconds to initialize map INFO:: 0.108 seconds for FFT INFO:: 0.026 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.032 seconds for contour map INFO:: 0.234 seconds in total (make-and-draw-map-with-reso-with-refmac-params "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) (another-level-from-map-molecule-number 2) Entered testcase - Sharpen map from map (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.074 seconds to read MTZ file INFO:: 0.042 seconds to initialize map INFO:: 0.07 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 3.31773e-12 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.006 seconds for contour map INFO:: 0.201 seconds in total INFO:: map file type was determined to be CCP4 type allocating space in read_ccp4_map attempting to read CCP4 map: test-3hfl.map closing CCP4 map: test-3hfl.map Map statistics: mean: 3.31773e-12 st.d: 0.260405 Map statistics: min: -1.03389, max: 1.71787 -0.965098 9 -0.82751 119 -0.689922 1019 -0.552334 4514 -0.414746 13139 -0.277158 28550 -0.13957 59504 -0.00198239 84317 0.135606 44993 0.273194 14815 0.410781 9178 0.548369 7021 0.685957 4753 0.823545 2717 0.961133 1265 1.09872 403 1.23631 108 1.3739 34 1.51149 18 1.64907 3 1.78666 1 Map mean: ........ 3.31773e-12 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 Entered testcase - Set Atom Attribute Test (set-atom-attribute 0 "A" 11 "" " CA " "" "x" 64.5) Entered testcase - Add Terminal Residue Test (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 6 read successfully INFO:: Masking around 41 atoms fitting terminal residue with rigid body refinement using 100 trials INFO:: Fitting terminal residue with individual rigid body fitting. INFO:: found better residue, score: 3.50214 INFO:: found better residue, score: 3.9272 INFO:: found better residue, score: 4.379 INFO:: found better residue, score: 4.61148 A 0 ALA N :: xyz = ( 49.2, 12.74, 4.454) A 0 ALA C :: xyz = ( 50.2, 13.69, 2.416) A 0 ALA CA :: xyz = ( 49.88, 13.9, 3.891) A 0 ALA O :: xyz = ( 51.28, 14.01, 1.91) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: Creating directory coot-backup INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Sep_10_12:19:02_2009_modification_0.pdb.gz (add-terminal-residue 6 "A" 1 1) (write-pdb-file 6 "regression-test-terminal-residue.pdb") In new_molecule_by_atom_selection has contains chain id A Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Thu_Sep_10_12:19:02_2009_modification_0.pdb.gz (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) Entered testcase - Select by Sphere Symmetry available for this molecule (n-chains 8) (chain_id 8 0) Sphere mol: there are 4 residues in chain "B" (resname-from-serial-number 8 "B" 0) (setnum-from-serial-number 8 "B" 0) (insertion-code-from-serial-number 8 "B" 0) (resname-from-serial-number 8 "B" 1) (setnum-from-serial-number 8 "B" 1) (insertion-code-from-serial-number 8 "B" 1) (resname-from-serial-number 8 "B" 2) (setnum-from-serial-number 8 "B" 2) (insertion-code-from-serial-number 8 "B" 2) (resname-from-serial-number 8 "B" 3) (setnum-from-serial-number 8 "B" 3) (insertion-code-from-serial-number 8 "B" 3) Found 20 sphere atoms Entered testcase - Test Views (go-to-view-number 0 1) Entered testcase - Label Atoms and Delete In new_molecule_by_atom_selection has contains chain id B Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (set-rotation-centre 31.464 21.413 14.824) N /10/B is not found in this molecule: (9) atom selection from tutorial-modern.pdb INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_12:19:02_2009_modification_0.pdb.gz (delete-residue 9 "B" 10 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_12:19:02_2009_modification_1.pdb.gz (delete-residue 9 "B" 11 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_12:19:02_2009_modification_2.pdb.gz (delete-residue 9 "B" 12 "") Entered testcase - Rotamer outliers (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rotamer-test-fragment.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rotamer-test-fragment.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 10 read successfully INFO:: Reading rotamer probability tables...Failed to read rotamer probability table for SER Failed to open /usr/share/coot/rama-data/rota500-ser.data Failed to read rotamer probability table for VAL Failed to open /usr/share/coot/rama-data/rota500-val.data Failed to read rotamer probability table for THR Failed to open /usr/share/coot/rama-data/rota500-thr.data Failed to read rotamer probability table for CYS Failed to open /usr/share/coot/rama-data/rota500-cys.data Failed to read rotamer probability table for PRO Failed to open /usr/share/coot/rama-data/rota500-pro.data Failed to read rotamer probability table for ASN Failed to open /usr/share/coot/rama-data/rota500-asn.data Failed to read rotamer probability table for ASP Failed to open /usr/share/coot/rama-data/rota500-asp.data Failed to read rotamer probability table for PHE Failed to open /usr/share/coot/rama-data/rota500-phetyr.data Failed to read rotamer probability table for TYR Failed to open /usr/share/coot/rama-data/rota500-phetyr.data Failed to read rotamer probability table for TRP Failed to open /usr/share/coot/rama-data/rota500-trp.data Failed to read rotamer probability table for HIS Failed to open /usr/share/coot/rama-data/rota500-his.data Failed to read rotamer probability table for ILE Failed to open /usr/share/coot/rama-data/rota500-ile.data Failed to read rotamer probability table for LEU Failed to open /usr/share/coot/rama-data/rota500-leu.data Failed to read rotamer probability table for MET Failed to open /usr/share/coot/rama-data/rota500-met.data Failed to read rotamer probability table for MSE Failed to open /usr/share/coot/rama-data/rota500-met.data Failed to read rotamer probability table for GLU Failed to open /usr/share/coot/rama-data/rota500-glu.data Failed to read rotamer probability table for GLN Failed to open /usr/share/coot/rama-data/rota500-gln.data Failed to read rotamer probability table for ARG Failed to open /usr/share/coot/rama-data/rota500-arg.data Failed to read rotamer probability table for LYS Failed to open /usr/share/coot/rama-data/rota500-lys.data PROBLEM in coordinates file? failed to find all atoms in ich number 0 THR 16 A failure rotamer test: ("A" 1 "" 0.0 "Rotamer not recognised") ("A" 2 "" 0.0 "Rotamer not recognised") ("A" 16 "" 0.0 "Missing Atoms") FAIL: Rotamer outliers Entered testcase - Alt Conf Occ Sum Reset (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/res098.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/res098.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 Cell: 57.374 57.374 87.384 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 11 read successfully For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 regularize: molecule 11 atom index 4 to 4 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 3 residues selected for refined and flanking residues created 6 bond restraints created 6 angle restraints created 0 plane restraints created 1 chiral vol restraints created 13 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 15 and 15 of chain X Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links INFO:: made 18 non-bonded restraints initial distortion_score: 8.98705 Initial Chi Squareds bonds: 0.149289 angles: 0.205078 torsions: N/A planes: 1.32634 non-bonded: 0 chiral vol: 0.0264636 rama plot: N/A Minimum found (iteration number 45) at 6.27253 Final Chi Squareds bonds: 0.00356353 angles: 0.290317 torsions: N/A planes: 0.654376 non-bonded: 0 chiral vol: 0.142707 rama plot: N/A SUCCESS TIME:: (dragged refinement): 2.776 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_res098.pdb_Thu_Sep_10_12:19:03_2009_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 test for closeness: 1.79999998211861 1.79999998211861 Entered testcase - Pepflip flips the correct alt confed atoms (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-pepflip-test.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-pepflip-test.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 12 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_alt-conf-pepflip-test.pdb_Thu_Sep_10_12:19:03_2009_modification_0.pdb.gz flipped 65 A Entered testcase - Correction of CISPEP test (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 13 read successfully (go-to-view-number 1 1) omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_12:19:03_2009_modification_0.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_12:19:03_2009_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 flipped 11 A INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_12:19:03_2009_modification_2.pdb.gz (mutate 11 "A" 13 "GLY") DEBUG:: check_dictionary_for_residues returns OK! INFO:: 4 residues selected for refined and flanking residues created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 21 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links INFO:: made 62 non-bonded restraints initial distortion_score: 565.206 Initial Chi Squareds bonds: 237.864 angles: 54.5685 torsions: N/A planes: 7.86923 non-bonded: 1.84407 chiral vol: 9.26976 rama plot: N/A Minimum found (iteration number 18) at -4818.58 Final Chi Squareds bonds: 1.04822 angles: 0.764573 torsions: N/A planes: 5.75545 non-bonded: 0 chiral vol: 0.00533487 rama plot: N/A SUCCESS TIME:: (dragged refinement): 3.496 Refinement elapsed time: 0.064 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_12:19:03_2009_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_12:19:03_2009_modification_4.pdb.gz (mutate 11 "A" 13 "LEU") ==== fitting residue 11 of chain A to map number 2 ====== INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_12:19:03_2009_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.41928 (auto-fit-best-rotamer 11 "" "" "A" 13 2 1 1) DEBUG:: check_dictionary_for_residues returns OK! INFO:: 4 residues selected for refined and flanking residues created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links INFO:: made 142 non-bonded restraints initial distortion_score: -6001 Initial Chi Squareds bonds: 1.01589 angles: 1.19474 torsions: N/A planes: 9.04357 non-bonded: 0 chiral vol: 0.00822091 rama plot: N/A Minimum found (iteration number 49) at -6078.09 Final Chi Squareds bonds: 1.1612 angles: 0.603749 torsions: N/A planes: 5.93809 non-bonded: 0 chiral vol: 0.297033 rama plot: N/A SUCCESS TIME:: (dragged refinement): 3.823 Refinement elapsed time: 0.055 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_12:19:03_2009_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... (write-pdb-file 13 "tmp-fixed-cis.pdb") /bin/grep CISPEPs: "3" Entered testcase - Refine Zone with Alt conf (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 14 read successfully (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.052 seconds to read MTZ file INFO:: 0.002 seconds to initialize map INFO:: 0.09 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.036 seconds for contour map INFO:: 0.19 seconds in total DEBUG:: check_dictionary_for_residues returns OK! INFO:: 3 residues selected for refined and flanking residues created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 10 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 72 and 72 of chain B Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links INFO:: made 12 non-bonded restraints initial distortion_score: -2784.62 Initial Chi Squareds bonds: 1.62991 angles: 1.14414 torsions: N/A planes: 0.831346 non-bonded: 0 chiral vol: 2.13751 rama plot: N/A Minimum found (iteration number 16) at -3085.72 Final Chi Squareds bonds: 2.46124 angles: 3.87881 torsions: N/A planes: 3.80237 non-bonded: 0.00908571 chiral vol: 4.58403 rama plot: N/A SUCCESS TIME:: (dragged refinement): 4.355 Refinement elapsed time: 0.031 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:05_2009_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... refined moved: d=0.595344045565208 Entered testcase - Sphere Refine (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 16 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Sep_10_12:19:05_2009_modification_0.pdb.gz (set-go-to-atom-molecule 16) imol: 16 residues: (("A" 93 "") ("A" 5 "") ("A" 3 "") ("A" 92 "")) DEUBG:: There are 64 atoms total (including flankers) created 27 bond restraints created 31 angle restraints created 1 plane restraints created 5 chiral vol restraints created 64 restraints INFO:: [spec: "A" 93 ""] [spec: "A" 92 ""] link_type :TRANS: Link restraints: 1 bond links 3 angle links 2 plane links Flanking residue restraints: 5 bond links 15 angle links 10 plane links INFO:: made 676 non-bonded restraints initial distortion_score: -15808.7 Initial Chi Squareds bonds: 1.8196 angles: 1.27384 torsions: N/A planes: 1.01372 non-bonded: 0 chiral vol: 0.658962 rama plot: N/A Minimum found (iteration number 44) at -16083.9 Final Chi Squareds bonds: 1.57653 angles: 0.571875 torsions: N/A planes: 0.762081 non-bonded: 0 chiral vol: 0.104681 rama plot: N/A SUCCESS TIME:: (dragged refinement): 4.984 Entered testcase - Rigid Body Refine Alt Conf Waters (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-waters.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-waters.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 17 read successfully masking....masking done INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_alt-conf-waters.pdb_Thu_Sep_10_12:19:05_2009_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... WARNING:: refine_zone: Can't get index for resno1: 2 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - Setting multiple atom attributes Entered testcase - Tweak Alt Confs on Active Residue (set-go-to-atom-molecule 0) (set-atom-string-attribute 0 "B" 58 "" " CB " "" "alt-conf" "B") Entered testcase - Backrub rotamer (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/backrub-fragment.pdb" 0) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/backrub-fragment.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 18 read successfully Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 18) INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_backrub-fragment.pdb_Thu_Sep_10_12:19:06_2009_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_backrub-fragment.pdb_Thu_Sep_10_12:19:06_2009_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. Entered testcase - Libcif horne (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/coords-B3A.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/coords-B3A.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 20 read successfully regularize: molecule 20 atom index 0 to 0 DEUBG:: check_dictionary_for_residues - problem... WARNING:: Failed to find restraints for :B3A: INFO:: 1 residues selected for refined and flanking residues created 0 bond restraints created 0 angle restraints created 0 plane restraints created 0 chiral vol restraints created 0 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links No restraints: regularize() ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/lib-B3A.cif not found. init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/lib-B3A.cif had no bond restraints regularize: molecule 20 atom index 0 to 0 DEUBG:: check_dictionary_for_residues - problem... WARNING:: Failed to find restraints for :B3A: INFO:: 1 residues selected for refined and flanking residues created 0 bond restraints created 0 angle restraints created 0 plane restraints created 0 chiral vol restraints created 0 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links No restraints: regularize() ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... There are 3 data in /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/lib-both.cif Read 28 atoms/links in restraints from /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/lib-both.cif regularize: molecule 20 atom index 0 to 0 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 10 non-bonded restraints initial distortion_score: 0.00371314 Initial Chi Squareds bonds: 0.00061433 angles: 0.000126593 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 8.51661e-06 rama plot: N/A Minimum found (iteration number 6) at 3.86343e-05 Final Chi Squareds bonds: 1.20485e-07 angles: 7.25441e-06 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 1.75988e-06 rama plot: N/A SUCCESS TIME:: (dragged refinement): 5.99 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_coords-B3A.pdb_Thu_Sep_10_12:19:06_2009_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - Refmac Parameters Storage (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "/RNASE3GMP/COMPLEX/FWT" "/RNASE3GMP/COMPLEX/PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.059 seconds to read MTZ file INFO:: 0.002 seconds to initialize map INFO:: 0.084 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.034 seconds for contour map INFO:: 0.188 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. Entered testcase - OXT is added before TER record - add only one (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/test-TER-OXT.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/test-TER-OXT.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/test-TER-OXT.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 22 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_test-TER-OXT.pdb_Thu_Sep_10_12:19:07_2009_modification_0.pdb.gz Added OXT at 1/A/14/ASP/ OXT altLoc :: segid :: pos: (33.1294,-9.08972,14.9163) B-factor: 45 (add-OXT-to-residue 22 14 "" "A") WARNING:: This residue already has an OXT - aborting (add-OXT-to-residue 22 14 "" "A") (write-pdb-file 22 "test-TER-OXT-added.pdb") found TER "TER 25 ASP A 14 " Entered testcase - The position of the oxygen after a mutation (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/val.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/val.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/val.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 23 read successfully INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_val.pdb_Thu_Sep_10_12:19:07_2009_modification_0.pdb.gz (mutate 3 "C" 23 "HIS") (write-pdb-file 23 "his.pdb") Entered testcase - Deleting (non-existing) Alt conf and Go To Atom [JED] failed to delete residue atoms A 88 :A: (delete-residue-with-altconf 0 "A" 88 "" "A") Entered testcase - Mask and difference map (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.059 seconds to read MTZ file INFO:: 0.003 seconds to initialize map INFO:: 0.085 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.032 seconds for contour map INFO:: 0.189 seconds in total (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.056 seconds to read MTZ file INFO:: 0.233 seconds to initialize map INFO:: 0.201 seconds for FFT INFO:: 0.019 seconds for statistics Map mean: ........ 1.18834e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.109 seconds for contour map INFO:: 0.618 seconds in total (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 0) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 26 read successfully INFO:: Masking around 64 atoms Map statistics: mean: -0.00140323 st.d: 0.305597 Map statistics: min: -0.875045, max: 2.97757 -0.77873 55 -0.586099 2468 -0.393468 24912 -0.200837 59810 -0.00820671 81565 0.184424 31729 0.377055 10140 0.569685 6763 0.762316 4842 0.954947 3073 1.14758 1603 1.34021 726 1.53284 283 1.72547 93 1.9181 24 2.11073 3 2.30336 5 2.49599 1 2.68862 0 2.88125 1 3.07389 0 (atom-info-string 26 "A" 20 "" " CA " "") (atom-info-string 26 "A" 21 "" " CA " "") (atom-info-string 26 "A" 22 "" " CA " "") (atom-info-string 26 "A" 23 "" " CA " "") (atom-info-string 26 "A" 24 "" " CA " "") (atom-info-string 26 "A" 25 "" " CA " "") (atom-info-string 26 "A" 26 "" " CA " "") (atom-info-string 26 "A" 27 "" " CA " "") (atom-info-string 26 "A" 28 "" " CA " "") (atom-info-string 26 "A" 29 "" " CA " "") (atom-info-string 26 "A" 30 "" " CA " "") (atom-info-string 26 "A" 1 "" " CA " "") (atom-info-string 26 "A" 2 "" " CA " "") (atom-info-string 26 "A" 3 "" " CA " "") (atom-info-string 26 "A" 4 "" " CA " "") (atom-info-string 26 "A" 5 "" " CA " "") (atom-info-string 26 "A" 6 "" " CA " "") (atom-info-string 26 "A" 7 "" " CA " "") (atom-info-string 26 "A" 8 "" " CA " "") (atom-info-string 26 "A" 9 "" " CA " "") (atom-info-string 26 "A" 10 "" " CA " "") high-values: (0.923012852668762 0.928160607814789 0.963148474693298 0.588746070861816 0.692066609859467 0.7519770860672 0.68085777759552 0.954908907413483 1.00084149837494 0.981854677200317 0.726146519184113) low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0) Map statistics: mean: -0.00140318 st.d: 0.0601239 Map statistics: min: -2.78832, max: 0.730463 -2.70035 2 -2.52441 2 -2.34847 2 -2.17253 1 -1.99659 3 -1.82065 2 -1.64471 8 -1.46877 10 -1.29283 37 -1.1169 76 -0.940957 122 -0.765018 193 -0.589079 261 -0.41314 329 -0.237201 473 -0.0612622 224025 0.114677 1297 0.290616 919 0.466554 308 0.642493 26 0.818432 0 diff-high-values: (0.00255923601798713 0.00100331113208085 0.00106650416273624 -0.00237782066687942 0.00169654644560069 7.11922300979495e-4 0.00212939688935876 0.00194922799710184 0.00229486566968262 6.56027928926051e-4 0.00835366826504469) diff-low-values: (-0.887997150421143 -0.79390150308609 -1.18933141231537 -1.06666219234467 -0.988452911376953 -0.759092688560486 -0.748683869838715 -0.650666296482086 -0.904519736766815 -0.545242130756378) Entered testcase - Simple Averaged maps (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.053 seconds to read MTZ file INFO:: 0.003 seconds to initialize map INFO:: 0.093 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.037 seconds for contour map INFO:: 0.196 seconds in total (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.057 seconds to read MTZ file INFO:: 0.453 seconds to initialize map INFO:: 0.429 seconds for FFT INFO:: 0.029 seconds for statistics Map mean: ........ 1.0992e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.07133 Map minimum: ..... -0.877519 INFO:: 0.168 seconds for contour map INFO:: 1.136 seconds in total Map statistics: mean: -4.27665e-07 st.d: 0.311072 Map statistics: min: -0.873369, max: 2.97503 -0.777159 58 -0.584739 2569 -0.392319 25676 -0.1999 61199 -0.00747969 77803 0.18494 32128 0.37736 10498 0.56978 7060 0.7622 5057 0.954619 3192 1.14704 1668 1.33946 756 1.53188 288 1.7243 102 1.91672 25 2.10914 4 2.30156 7 2.49398 3 2.6864 1 2.87882 1 3.07124 1 Map statistics: mean: 4.28879e-07 st.d: 0.00106883 Map statistics: min: -0.00685638, max: 0.0119245 -0.00638686 26 -0.00544782 84 -0.00450877 335 -0.00356973 1277 -0.00263068 4286 -0.00169164 14039 -0.000752594 59649 0.000186451 105523 0.0011255 30405 0.00206454 7562 0.00300358 2850 0.00394263 1180 0.00488167 486 0.00582072 253 0.00675976 93 0.00769881 28 0.00863785 13 0.00957689 4 0.0105159 2 0.011455 1 0.012394 0 INFO:: map sigmas: normal 0.311072051525116 and diff-map: 0.00106883211992681 Entered testcase - Make a glycosidic linkage (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/multi-carbo-coot-2.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/multi-carbo-coot-2.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/multi-carbo-coot-2.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 33 read successfully bond-length: 2.97694066606539: regularize: molecule 33 atom index 0 to 20 There are 2 data in /usr/share/ccp4//data/monomers/f/FUC-A-L.cif There are 2 data in /usr/share/ccp4//data/monomers/n/NAG-B-D.cif DEBUG:: check_dictionary_for_residues returns OK! INFO:: 2 residues selected for refined and flanking residues created 46 bond restraints created 71 angle restraints created 1 plane restraints created 8 chiral vol restraints created 126 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A INFO:: glycosidic_linkage type :BETA1-4: INFO:: No chem link for groups L-pyranose D-pyranose and comp_ids FUC NAG Link restraints: 1 bond links 3 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 1560 non-bonded restraints initial distortion_score: 6392.77 Initial Chi Squareds bonds: 127.526 angles: 4.95566 torsions: N/A planes: 0.00816956 non-bonded: 0.0150013 chiral vol: 1.112 rama plot: N/A Minimum found (iteration number 175) at 246.274 Final Chi Squareds bonds: 1.72113 angles: 1.79949 torsions: N/A planes: 0.00099634 non-bonded: 0.0149161 chiral vol: 1.11853 rama plot: N/A SUCCESS TIME:: (dragged refinement): 13.683 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_multi-carbo-coot-2.pdb_Thu_Sep_10_12:19:14_2009_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... bond-length: 1.44038255526854: Entered testcase - Test for flying hydrogens on undo (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-VAL.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-VAL.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 34 read successfully regularize: molecule 34 atom index 0 to 0 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 132 non-bonded restraints initial distortion_score: 35.0317 Initial Chi Squareds bonds: 0.268606 angles: 0.0269163 torsions: N/A planes: N/A non-bonded: 0.230261 chiral vol: 0.20393 rama plot: N/A Minimum found (iteration number 10) at 0.247096 Final Chi Squareds bonds: 0.00015527 angles: 0.00897939 torsions: N/A planes: N/A non-bonded: 1.53575e-09 chiral vol: 0.0204374 rama plot: N/A SUCCESS TIME:: (dragged refinement): 14.461 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_12:19:15_2009_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... INFO:: undo molecule number set to: 34 (set-undo-molecule 34) INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_12:19:15_2009_modification_1.pdb.gz restoring from backup 2 2 Reading coordinate file: coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_12:19:15_2009_modification_0.pdb.gz PDB file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_12:19:15_2009_modification_0.pdb.gz has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 (apply-undo) regularize: molecule 34 atom index 0 to 0 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 132 non-bonded restraints initial distortion_score: 35.0317 Initial Chi Squareds bonds: 0.268606 angles: 0.0269163 torsions: N/A planes: N/A non-bonded: 0.230261 chiral vol: 0.20393 rama plot: N/A Minimum found (iteration number 10) at 0.247096 Final Chi Squareds bonds: 0.00015527 angles: 0.00897939 torsions: N/A planes: N/A non-bonded: 1.53575e-09 chiral vol: 0.0204374 rama plot: N/A SUCCESS TIME:: (dragged refinement): 14.599 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_12:19:15_2009_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - Test for mangling of hydrogen names from a PDB v 3.0 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3ins-6B-3.0.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3ins-6B-3.0.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3ins-6B-3.0.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 35 read successfully regularize: molecule 35 atom index 0 to 0 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues Unknown element : D: created 16 bond restraints created 28 angle restraints created 0 plane restraints created 1 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 6 and 6 of chain B Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 254 non-bonded restraints initial distortion_score: 20907.8 Initial Chi Squareds bonds: 31.4514 angles: 12.6131 torsions: N/A planes: N/A non-bonded: 78.9403 chiral vol: 0.567548 rama plot: N/A Minimum found (iteration number 26) at 0.252086 Final Chi Squareds bonds: 0.000107256 angles: 0.00825211 torsions: N/A planes: N/A non-bonded: 5.06464e-08 chiral vol: 0.0192984 rama plot: N/A SUCCESS TIME:: (dragged refinement): 15.72 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_3ins-6B-3.0.pdb_Thu_Sep_10_12:19:16_2009_modification_0.pdb.gz INFO:: replace_coords: 19 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - update monomer restraints In new_molecule_by_atom_selection has contains chain id A Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 28 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 78 non-bonded restraints initial distortion_score: -1120.52 Initial Chi Squareds bonds: 1.16837 angles: 0.718389 torsions: N/A planes: 9.33775 non-bonded: 40.0438 chiral vol: 0.995302 rama plot: N/A Minimum found (iteration number 48) at -4202.57 Final Chi Squareds bonds: 5.00835 angles: 0.722604 torsions: N/A planes: 0.917534 non-bonded: 0.0786912 chiral vol: 0.995449 rama plot: N/A SUCCESS TIME:: (dragged refinement): 15.828 Refinement elapsed time: 0.047 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_12:19:16_2009_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Bond-length: 2.26496220633885: pass intermediate 2.8 tolerance test DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 12 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 74 non-bonded restraints initial distortion_score: -3037.32 Initial Chi Squareds bonds: 102.207 angles: 0.722604 torsions: N/A planes: 0.917534 non-bonded: 0 chiral vol: 0.995449 rama plot: N/A Minimum found (iteration number 49) at -4306.6 Final Chi Squareds bonds: 1.22279 angles: 0.808124 torsions: N/A planes: 2.56077 non-bonded: 0 chiral vol: 0.995579 rama plot: N/A SUCCESS TIME:: (dragged refinement): 15.891 Refinement elapsed time: 0.036 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_12:19:16_2009_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... OK plane atom " CB " Bond-length: 1.53218859531565: Entered testcase - Refinement OK with zero bond esd (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-ACT.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-ACT.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 37 read successfully There are 2 data in /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_ACT.cif Read 7 atoms/links in restraints from /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_ACT.cif DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 6 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints created 15 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 0 non-bonded restraints initial distortion_score: 108.409 Initial Chi Squareds bonds: 0.00014374 angles: 4.27673e-05 torsions: N/A planes: 0 non-bonded: N/A chiral vol: N/A rama plot: N/A Minimum found (iteration number 66) at -1093.91 Final Chi Squareds bonds: 0.23613 angles: 0.64763 torsions: N/A planes: 0.000243983 non-bonded: N/A chiral vol: N/A rama plot: N/A SUCCESS TIME:: (dragged refinement): 16.563 Refinement elapsed time: 0.068 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-ACT.pdb_Thu_Sep_10_12:19:17_2009_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - Change Chain IDs and Chain Sorting (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 38 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_2.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_3.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_4.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_5.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_6.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_7.pdb.gz (n-chains 38) (chain_id 38 0) (chain_id 38 1) (chain_id 38 2) (chain_id 38 3) (chain_id 38 4) (chain_id 38 5) (chain_id 38 6) (chain_id 38 7) (chain_id 38 8) Entered testcase - Replace Fragment Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) In new_molecule_by_atom_selection has contains chain id A In new_molecule_by_atom_selection has contains chain id B Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:18_2009_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. (replace-fragement 39 "//A70-80") distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) Entered testcase - Residues in Region of Residue found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) found 0 neighbours () Entered testcase - Residues in region of a point (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 41 read successfully Entered testcase - Empty molecule on type selection in new_molecule_by_residue_type_selection Something bad happened - No residues selected (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") in new_molecule_by_residue_type_selection Something bad happened - No residues selected (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") Entered testcase - Set Rotamer INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:19_2009_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint Entered testcase - Rotamer names and scores are correct (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 42 read successfully (backup-state 42) (turn-off-backup 42) (rotamer-score 42 "A" 28 "") Rotamer 0 : "m-85" 44.0 fail on rotamer probability: result: 44.0 should be: 100 FAIL: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 50/87 Molecule 43 read successfully INFO:: aligning to mol number 43chain: A ------------------------------------------------- chain A ------------------------------------------------- INFO:: input model sequence:GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence:DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID > /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID > target seq: DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 160 There are 8 single_insertions INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_rnase-A-needs-an-insertion.pdb_Thu_Sep_10_12:19:21_2009_modification_0.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 The alignment resulted in the following Insertions (coalesced): from 1 to 4 ASP VAL SER from 11 to 14 LEU PRO PRO from 62 to 64 PRO GLY Insertions (singles): [spec: "A" 1 ""] -> ASP [spec: "A" 2 ""] -> VAL [spec: "A" 3 ""] -> SER [spec: "A" 11 ""] -> LEU [spec: "A" 12 ""] -> PRO [spec: "A" 13 ""] -> PRO [spec: "A" 62 ""] -> PRO [spec: "A" 63 ""] -> GLY Deletions: [spec: "A" 24 ""] [spec: "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions (write-pdb-file 43 "mutated.pdb") ::::: (43 "A" 1 "") #f #f ::::: (43 "A" 4 "") #t #t ::::: (43 "A" 59 "") #t #t ::::: (43 "A" 60 "") #f #f ::::: (43 "A" 61 "") #f #f ::::: (43 "A" 92 "") #t #t ::::: (43 "A" 94 "") #f #f Entered testcase - Autofit Rotamer on Residues with Insertion codes (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb3hfl.ent" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb3hfl.ent PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb3hfl.ent has been read. No Spacegroup found for this PDB file Cell: 54.79 74.82 78.95 90 101.82 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 44 read successfully (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.051 seconds to read MTZ file INFO:: 0.003 seconds to initialize map INFO:: 0.074 seconds for FFT INFO:: 0.011 seconds for statistics Map mean: ........ 3.31773e-12 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.017 seconds for contour map INFO:: 0.156 seconds in total ==== fitting residue 52A of chain H to map number 45 ====== INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb3hfl.ent_Thu_Sep_10_12:19:22_2009_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.82781 (auto-fit-best-rotamer 52 "" "A" "H" 44 45 0 0) INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb3hfl.ent_Thu_Sep_10_12:19:22_2009_modification_1.pdb.gz Entered testcase - RNA base has correct residue type after mutation INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 request std_res of type Gr and got Gr coot::util::mutate_base Gr with std Gr INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 request std_res of type Ar and got Ar coot::util::mutate_base Ar with std Ar INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 request std_res of type Cr and got Cr coot::util::mutate_base Cr with std Cr INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 request std_res of type Ur and got Ur coot::util::mutate_base Ur with std Ur INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 request std_res of type Cr and got Cr coot::util::mutate_base Cr with std Cr INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 request std_res of type Ur and got Ur coot::util::mutate_base Ur with std Ur INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 request std_res of type Ar and got Ar coot::util::mutate_base Ar with std Ar INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 request std_res of type Gr and got Gr coot::util::mutate_base Gr with std Gr INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 request std_res of type Cr and got Cr coot::util::mutate_base Cr with std Cr INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 request std_res of type Ur and got Ur coot::util::mutate_base Ur with std Ur INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 request std_res of type Gr and got Gr coot::util::mutate_base Gr with std Gr INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 request std_res of type Ar and got Ar coot::util::mutate_base Ar with std Ar INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 request std_res of type Gr and got Gr coot::util::mutate_base Gr with std Gr INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 request std_res of type Ar and got Ar coot::util::mutate_base Ar with std Ar INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 request std_res of type Ur and got Ur coot::util::mutate_base Ur with std Ur INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 request std_res of type Cr and got Cr coot::util::mutate_base Cr with std Cr !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Thu_Sep_10_12:19:22_2009_modification_0.pdb.gz (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") INFO:: backup file coot-backup/Ideal-A-form-RNA_Thu_Sep_10_12:19:22_2009_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.269035 rms devi: 0.337196 max devi: 0.547544 min devi: 0.0817551 mutated base to type "Cr" Entered testcase - DNA bases are the correct residue type after mutation INFO:: 5 matched atoms had: mean devi: 0.00589883 rms devi: 0.00670957 max devi: 0.0101325 min devi: 0.00258111 request std_res of type Gd and got Gd coot::util::mutate_base Gd with std Gd INFO:: 5 matched atoms had: mean devi: 0.00725623 rms devi: 0.00778801 max devi: 0.0125644 min devi: 0.00456024 request std_res of type Ad and got Ad coot::util::mutate_base Ad with std Ad INFO:: 5 matched atoms had: mean devi: 0.271793 rms devi: 0.336384 max devi: 0.533839 min devi: 0.0878288 request std_res of type Cd and got Cd coot::util::mutate_base Cd with std Cd INFO:: 5 matched atoms had: mean devi: 0.26776 rms devi: 0.326512 max devi: 0.505569 min devi: 0.10459 request std_res of type Td and got Td coot::util::mutate_base Td with std Td INFO:: 5 matched atoms had: mean devi: 0.271823 rms devi: 0.336416 max devi: 0.53388 min devi: 0.0879009 request std_res of type Cd and got Cd coot::util::mutate_base Cd with std Cd INFO:: 5 matched atoms had: mean devi: 0.267791 rms devi: 0.326544 max devi: 0.505617 min devi: 0.104522 request std_res of type Td and got Td coot::util::mutate_base Td with std Td INFO:: 5 matched atoms had: mean devi: 0.00717866 rms devi: 0.00770023 max devi: 0.0124098 min devi: 0.00457508 request std_res of type Ad and got Ad coot::util::mutate_base Ad with std Ad INFO:: 5 matched atoms had: mean devi: 0.00574436 rms devi: 0.00657052 max devi: 0.0099594 min devi: 0.0024248 request std_res of type Gd and got Gd coot::util::mutate_base Gd with std Gd INFO:: 5 matched atoms had: mean devi: 0.271762 rms devi: 0.336353 max devi: 0.533797 min devi: 0.0877567 request std_res of type Cd and got Cd coot::util::mutate_base Cd with std Cd INFO:: 5 matched atoms had: mean devi: 0.267729 rms devi: 0.326479 max devi: 0.505521 min devi: 0.104657 request std_res of type Td and got Td coot::util::mutate_base Td with std Td INFO:: 5 matched atoms had: mean devi: 0.00585391 rms devi: 0.00666923 max devi: 0.0100827 min devi: 0.00253528 request std_res of type Gd and got Gd coot::util::mutate_base Gd with std Gd INFO:: 5 matched atoms had: mean devi: 0.00722485 rms devi: 0.00775255 max devi: 0.0125025 min devi: 0.00456535 request std_res of type Ad and got Ad coot::util::mutate_base Ad with std Ad INFO:: 5 matched atoms had: mean devi: 0.00580961 rms devi: 0.00662938 max devi: 0.0100332 min devi: 0.00249036 request std_res of type Gd and got Gd coot::util::mutate_base Gd with std Gd INFO:: 5 matched atoms had: mean devi: 0.00719394 rms devi: 0.00771755 max devi: 0.0124407 min devi: 0.00457156 request std_res of type Ad and got Ad coot::util::mutate_base Ad with std Ad INFO:: 5 matched atoms had: mean devi: 0.267807 rms devi: 0.326561 max devi: 0.505641 min devi: 0.104488 request std_res of type Td and got Td coot::util::mutate_base Td with std Td INFO:: 5 matched atoms had: mean devi: 0.27187 rms devi: 0.336463 max devi: 0.533942 min devi: 0.088009 request std_res of type Cd and got Cd coot::util::mutate_base Cd with std Cd !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Sep_10_12:19:22_2009_modification_0.pdb.gz (ideal-nucleic-acid "DNA" "A" 0 "GACTCTAG") INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Sep_10_12:19:22_2009_modification_1.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.270191 rms devi: 0.336363 max devi: 0.538427 min devi: 0.0854029 mutated base to type "Cd" INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Sep_10_12:19:22_2009_modification_2.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.271895 rms devi: 0.336278 max devi: 0.534478 min devi: 0.0923473 mutated base to type "Gd" INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Sep_10_12:19:22_2009_modification_3.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.0043292 rms devi: 0.00481764 max devi: 0.00738267 min devi: 0.00186162 mutated base to type "Ad" INFO:: backup file coot-backup/Ideal-A-form-DNA_Thu_Sep_10_12:19:22_2009_modification_4.pdb.gz INFO:: 5 matched atoms had: mean devi: 0.265718 rms devi: 0.326008 max devi: 0.501859 min devi: 0.0926641 mutated base to type "Td" Entered testcase - SegIDs are correct after mutate Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) INFO:: mutate 32 A to a LYS INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:23_2009_modification_0.pdb.gz (mutate 32 "A" 48 "LYS") Entered testcase - TER on water chain is removed on adding a water by hand (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/some-waters-with-ter.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/some-waters-with-ter.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/some-waters-with-ter.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 49 read successfully (set-rotation-centre 3 4 5) INFO:: adding atom of type Water at (3,4,5) INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_some-waters-with-ter.pdb_Thu_Sep_10_12:19:23_2009_modification_0.pdb.gz 1/D/79/HOH/ O altLoc :: segid :: pos: (3,4,5) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (write-pdb-file 49 "tmp-with-new-water.pdb") Entered testcase - TER on water chain is removed on adding waters automatically (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tm+some-waters.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tm+some-waters.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tm+some-waters.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 50 read successfully Protein centre at: xyz = ( 41.57, 8.745, 12.89) using sigma cut off 2 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.311501 INFO:: Using density cut-off: 0.623002 (2 sigma) (mean -0.0337018 stdev: 0.146071) INFO:: Using water to protein distance limits: 2.2 3.4 Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( 59.91, 3.027, -4.296) is too big to be water INFO:: cluster at xyz = ( 70.01, 19.05, 18.63) is too big to be water INFO:: found 48 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tm+some-waters.pdb_Thu_Sep_10_12:19:24_2009_modification_0.pdb.gz INFO:: Adding to solvent chain: D (write-pdb-file 50 "auto-waters.pdb") (write-pdb-file 50 "tmp-with-new-water.pdb") Entered testcase - Arrange waters round protein (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/water-test-no-cell.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/water-test-no-cell.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/water-test-no-cell.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 51 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_water-test-no-cell.pdb_Thu_Sep_10_12:19:25_2009_modification_0.pdb.gz No symmetry available INFO:: moved 0 water molecules (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pathological-water-test.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pathological-water-test.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pathological-water-test.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 52 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pathological-water-test.pdb_Thu_Sep_10_12:19:26_2009_modification_0.pdb.gz INFO:: moved 181 water molecules (write-pdb-file 52 "waters-moved-failure.pdb") Entered testcase - Correct Segid After Add Terminal Residue Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.062 seconds to read MTZ file INFO:: 0.002 seconds to initialize map INFO:: 0.09 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.032 seconds for contour map INFO:: 0.196 seconds in total INFO:: Masking around 58 atoms fitting terminal residue with rigid body refinement using 100 trials INFO:: Fitting terminal residue with individual rigid body fitting. INFO:: found better residue, score: 5.5329 INFO:: found better residue, score: 7.65684 INFO:: found better residue, score: 10.2175 A 94 ALA N :: xyz = ( 58.94, 2.905, -1.681) A 94 ALA C :: xyz = ( 60.31, 1.87, -3.439) A 94 ALA CA :: xyz = ( 59.96, 1.903, -1.956) A 94 ALA O :: xyz = ( 61.48, 1.739, -3.805) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:27_2009_modification_0.pdb.gz DEBUG:: insert_coords_internal() add residue 0 of 8 1/A/93/ASP/ N altLoc :: segid :A: pos: (57.032,5.59,-0.723) B-factor: 10.7 1 of 8 1/A/93/ASP/ CA altLoc :: segid :A: pos: (56.859,4.651,-1.821) B-factor: 9.77 2 of 8 1/A/93/ASP/ CB altLoc :: segid :A: pos: (56.223,5.398,-3.023) B-factor: 7.83 3 of 8 1/A/93/ASP/ CG altLoc :: segid :A: pos: (56.097,4.54,-4.207) B-factor: 10.96 4 of 8 1/A/93/ASP/ OD1 altLoc :: segid :A: pos: (55.497,4.981,-5.242) B-factor: 10.83 5 of 8 1/A/93/ASP/ OD2 altLoc :: segid :A: pos: (56.623,3.401,-4.248) B-factor: 12.14 6 of 8 1/A/93/ASP/ C altLoc :: segid :A: pos: (58.283,4.084,-2.167) B-factor: 10.98 7 of 8 1/A/93/ASP/ O altLoc :: segid :A: pos: (59.091,4.976,-2.587) B-factor: 10.33 (add-terminal-residue 53 "A" 93 1) Entered testcase - Correct Segid after NCS residue range copy Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) Entered testcase - Merge Water Chains (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 56 read successfully (backup-state 56) (turn-off-backup 56) INFO:: adding atom of type Water at (41.5953,8.68654,12.9093) 0//-32767/HOH/ O altLoc :: segid :: pos: (41.5953,8.68654,12.9093) B-factor: 45 added to molecule (and new chain) (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 43.5953 8.68654 12.9093) INFO:: adding atom of type Water at (43.5953,8.68654,12.9093) 1/C/2/HOH/ O altLoc :: segid :: pos: (43.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 45.5953 8.68654 12.9093) INFO:: adding atom of type Water at (45.5953,8.68654,12.9093) 1/C/3/HOH/ O altLoc :: segid :: pos: (45.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 47.5953 8.68654 12.9093) INFO:: adding atom of type Water at (47.5953,8.68654,12.9093) 1/C/4/HOH/ O altLoc :: segid :: pos: (47.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 49.5953 8.68654 12.9093) INFO:: adding atom of type Water at (49.5953,8.68654,12.9093) 1/C/5/HOH/ O altLoc :: segid :: pos: (49.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 51.5953 8.68654 12.9093) (renumber-residue-range 56 "D" 1 5 10) INFO:: adding atom of type Water at (51.5953,8.68654,12.9093) 1/D/16/HOH/ O altLoc :: segid :: pos: (51.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 53.5953 8.68654 12.9093) INFO:: adding atom of type Water at (53.5953,8.68654,12.9093) 1/D/17/HOH/ O altLoc :: segid :: pos: (53.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 55.5953 8.68654 12.9093) INFO:: adding atom of type Water at (55.5953,8.68654,12.9093) 1/D/18/HOH/ O altLoc :: segid :: pos: (55.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 57.5953 8.68654 12.9093) INFO:: adding atom of type Water at (57.5953,8.68654,12.9093) 1/D/19/HOH/ O altLoc :: segid :: pos: (57.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 59.5953 8.68654 12.9093) INFO:: adding atom of type Water at (59.5953,8.68654,12.9093) 1/D/20/HOH/ O altLoc :: segid :: pos: (59.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 61.5953 8.68654 12.9093) (renumber-residue-range 56 "E" 11 15 5) INFO:: adding atom of type Water at (61.5953,8.68654,12.9093) 1/D/21/HOH/ O altLoc :: segid :: pos: (61.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 63.5953 8.68654 12.9093) INFO:: adding atom of type Water at (63.5953,8.68654,12.9093) 1/D/22/HOH/ O altLoc :: segid :: pos: (63.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 65.5953 8.68654 12.9093) INFO:: adding atom of type Water at (65.5953,8.68654,12.9093) 1/D/23/HOH/ O altLoc :: segid :: pos: (65.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 67.5953 8.68654 12.9093) INFO:: adding atom of type Water at (67.5953,8.68654,12.9093) 1/D/24/HOH/ O altLoc :: segid :: pos: (67.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 69.5953 8.68654 12.9093) INFO:: adding atom of type Water at (69.5953,8.68654,12.9093) 1/D/25/HOH/ O altLoc :: segid :: pos: (69.5953,8.68654,12.9093) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 71.5953 8.68654 12.9093) (renumber-residue-range 56 "F" 16 20 2) (n-chains 56) (chain_id 56 0) (chain_id 56 1) (chain_id 56 2) (chain_id 56 3) (chain_id 56 4) (is-solvent-chain-p 56 "A") (is-solvent-chain-p 56 "B") (is-solvent-chain-p 56 "D") (is-solvent-chain-p 56 "E") (is-solvent-chain-p 56 "F") (setnum-from-serial-number 56 "D" 4) (renumber-residue-range 56 "E" 1 5 5) (setnum-from-serial-number 56 "D" 9) (renumber-residue-range 56 "F" 1 10 10) (turn-on-backup 56) (n-chains 56) (chain_id 56 2) (setnum-from-serial-number 56 "D" 0) (setnum-from-serial-number 56 "D" 14) Entered testcase - LSQ by atom Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) INFO:: Matching/moving molecule number 58 to 57 INFO:: LSQ matched 4 atoms INFO:: 4 matched atoms had: mean devi: 0.0353197 rms devi: 0.0377881 max devi: 0.0545286 min devi: 0.016676 INFO:: Axis orientation: ( 0.9786, 0.1755, -0.1076) INFO:: Rotation in CCP4 Polar Angles: Polar = (83.8253,-169.833,67.7313) INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:19:29_2009_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.9737, 0.007115, -0.2278| | 0.2062, 0.3981, 0.8939| | 0.09703, -0.9173, 0.3861| ( 37.45, -16.6, 12.88) INFO:: fractional coordinates matrix: | 0.9737, 0.008587, -0.1361| | 0.1708, 0.3981, 0.4427| | 0.1623, -1.852, 0.3861| ( 0.577, -0.2119, 0.3319) Entered testcase - Phosphate distance in pucker analysis is sane (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2goz-manip.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2goz-manip.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2goz-manip.pdb has been read. Spacegroup: C 1 2 1 Cell: 49.886 69.21 60.076 90 111.83 90 INFO:: Found 1 models Model 1 had 7 links Symmetry available for this molecule INFO:: NCS chain comparison 10/85 Molecule 59 read successfully Ended 01-pdb+mtz.scm Running 02-shelx.scm ... Entered testcase - Read small molecule .res file (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/HOF.RES" 1) SFAC LINE: SFAC C H N O S INFO:: CELL set to 5.9028 13.6977 9.2374 90 98.211 90 INFO:: set space group to :P 1 21/c 1: READ-INS:: Spacegroup: P 1 21/c 1 INFO:: chain has 1 residues Symmetry available for this molecule Molecule 60 read successfully (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/HOF.RES") Entered testcase - Read hollander small molecule .res file (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/hollander.ins" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O CO INFO:: CELL set to 34.3243 34.3243 11.0887 90 90 90 INFO:: set space group to :I 41 2 2: READ-INS:: Spacegroup: I 41 2 2 INFO:: chain has 1 residues Symmetry available for this molecule Molecule 61 read successfully (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/hollander.ins") INFO:: spacegroup: I 41 2 2 Entered testcase - read shelx insulin with fcf (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/insulin.res" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.726 77.726 77.726 90 90 90 INFO:: set space group to :I 21 3: READ-INS:: Spacegroup: I 21 3 INFO:: chain has 120 residues Symmetry available for this molecule Molecule 62 read successfully (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/insulin.res") /usr/bin/awk exit status: 0 got cell from cif: Cell (77.726,77.726,77.726, 90, 90, 90) Found symmetry equivalents..... INFO:: Found cif symmetry operator x, y, z INFO:: Found cif symmetry operator -x+1/2, -y, z+1/2 INFO:: Found cif symmetry operator -x, y+1/2, -z+1/2 INFO:: Found cif symmetry operator x+1/2, -y+1/2, -z INFO:: Found cif symmetry operator z, x, y INFO:: Found cif symmetry operator z+1/2, -x+1/2, -y INFO:: Found cif symmetry operator -z+1/2, -x, y+1/2 INFO:: Found cif symmetry operator -z, x+1/2, -y+1/2 INFO:: Found cif symmetry operator y, z, x INFO:: Found cif symmetry operator -y, z+1/2, -x+1/2 INFO:: Found cif symmetry operator y+1/2, -z+1/2, -x INFO:: Found cif symmetry operator -y+1/2, -z, x+1/2 INFO:: Found cif symmetry operator x+1/2, y+1/2, z+1/2 INFO:: Found cif symmetry operator -x+1, -y+1/2, z+1 INFO:: Found cif symmetry operator -x+1/2, y+1, -z+1 INFO:: Found cif symmetry operator x+1, -y+1, -z+1/2 INFO:: Found cif symmetry operator z+1/2, x+1/2, y+1/2 INFO:: Found cif symmetry operator z+1, -x+1, -y+1/2 INFO:: Found cif symmetry operator -z+1, -x+1/2, y+1 INFO:: Found cif symmetry operator -z+1/2, x+1, -y+1 INFO:: Found cif symmetry operator y+1/2, z+1/2, x+1/2 INFO:: Found cif symmetry operator -y+1/2, z+1, -x+1 INFO:: Found cif symmetry operator y+1, -z+1, -x+1/2 INFO:: Found cif symmetry operator -y+1, -z+1/2, x+1 INFO:: space_group from symm ops in cif: I 21 3 got cell from cif: Cell (77.726,77.726,77.726, 90, 90, 90) Found symmetry equivalents..... INFO:: Found cif symmetry operator x, y, z INFO:: Found cif symmetry operator -x+1/2, -y, z+1/2 INFO:: Found cif symmetry operator -x, y+1/2, -z+1/2 INFO:: Found cif symmetry operator x+1/2, -y+1/2, -z INFO:: Found cif symmetry operator z, x, y INFO:: Found cif symmetry operator z+1/2, -x+1/2, -y INFO:: Found cif symmetry operator -z+1/2, -x, y+1/2 INFO:: Found cif symmetry operator -z, x+1/2, -y+1/2 INFO:: Found cif symmetry operator y, z, x INFO:: Found cif symmetry operator -y, z+1/2, -x+1/2 INFO:: Found cif symmetry operator y+1/2, -z+1/2, -x INFO:: Found cif symmetry operator -y+1/2, -z, x+1/2 INFO:: Found cif symmetry operator x+1/2, y+1/2, z+1/2 INFO:: Found cif symmetry operator -x+1, -y+1/2, z+1 INFO:: Found cif symmetry operator -x+1/2, y+1, -z+1 INFO:: Found cif symmetry operator x+1, -y+1, -z+1/2 INFO:: Found cif symmetry operator z+1/2, x+1/2, y+1/2 INFO:: Found cif symmetry operator z+1, -x+1, -y+1/2 INFO:: Found cif symmetry operator -z+1, -x+1/2, y+1 INFO:: Found cif symmetry operator -z+1/2, x+1, -y+1 INFO:: Found cif symmetry operator y+1/2, z+1/2, x+1/2 INFO:: Found cif symmetry operator -y+1/2, z+1, -x+1 INFO:: Found cif symmetry operator y+1, -z+1, -x+1/2 INFO:: Found cif symmetry operator -y+1, -z+1/2, x+1 INFO:: space_group from symm ops in cif: I 21 3 import_hkl_info read 16736 hkls 16736 calculated data read on close_read() Read 16735 from CIF file (sigmaa). sigmaa and scaling... initializing map...done. doing fft...done. Mean and sigma of map from CIF file (make_map_from_cif): -5.04462e-05 and 0.305067 Reading cif file (with phases - diff) : /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/insulin.fcf.cif got cell from cif: Cell (77.726,77.726,77.726, 90, 90, 90) Found symmetry equivalents..... INFO:: Found cif symmetry operator x, y, z INFO:: Found cif symmetry operator -x+1/2, -y, z+1/2 INFO:: Found cif symmetry operator -x, y+1/2, -z+1/2 INFO:: Found cif symmetry operator x+1/2, -y+1/2, -z INFO:: Found cif symmetry operator z, x, y INFO:: Found cif symmetry operator z+1/2, -x+1/2, -y INFO:: Found cif symmetry operator -z+1/2, -x, y+1/2 INFO:: Found cif symmetry operator -z, x+1/2, -y+1/2 INFO:: Found cif symmetry operator y, z, x INFO:: Found cif symmetry operator -y, z+1/2, -x+1/2 INFO:: Found cif symmetry operator y+1/2, -z+1/2, -x INFO:: Found cif symmetry operator -y+1/2, -z, x+1/2 INFO:: Found cif symmetry operator x+1/2, y+1/2, z+1/2 INFO:: Found cif symmetry operator -x+1, -y+1/2, z+1 INFO:: Found cif symmetry operator -x+1/2, y+1, -z+1 INFO:: Found cif symmetry operator x+1, -y+1, -z+1/2 INFO:: Found cif symmetry operator z+1/2, x+1/2, y+1/2 INFO:: Found cif symmetry operator z+1, -x+1, -y+1/2 INFO:: Found cif symmetry operator -z+1, -x+1/2, y+1 INFO:: Found cif symmetry operator -z+1/2, x+1, -y+1 INFO:: Found cif symmetry operator y+1/2, z+1/2, x+1/2 INFO:: Found cif symmetry operator -y+1/2, z+1, -x+1 INFO:: Found cif symmetry operator y+1, -z+1, -x+1/2 INFO:: Found cif symmetry operator -y+1, -z+1/2, x+1 INFO:: space_group from symm ops in cif: I 21 3 got cell from cif: Cell (77.726,77.726,77.726, 90, 90, 90) Found symmetry equivalents..... INFO:: Found cif symmetry operator x, y, z INFO:: Found cif symmetry operator -x+1/2, -y, z+1/2 INFO:: Found cif symmetry operator -x, y+1/2, -z+1/2 INFO:: Found cif symmetry operator x+1/2, -y+1/2, -z INFO:: Found cif symmetry operator z, x, y INFO:: Found cif symmetry operator z+1/2, -x+1/2, -y INFO:: Found cif symmetry operator -z+1/2, -x, y+1/2 INFO:: Found cif symmetry operator -z, x+1/2, -y+1/2 INFO:: Found cif symmetry operator y, z, x INFO:: Found cif symmetry operator -y, z+1/2, -x+1/2 INFO:: Found cif symmetry operator y+1/2, -z+1/2, -x INFO:: Found cif symmetry operator -y+1/2, -z, x+1/2 INFO:: Found cif symmetry operator x+1/2, y+1/2, z+1/2 INFO:: Found cif symmetry operator -x+1, -y+1/2, z+1 INFO:: Found cif symmetry operator -x+1/2, y+1, -z+1 INFO:: Found cif symmetry operator x+1, -y+1, -z+1/2 INFO:: Found cif symmetry operator z+1/2, x+1/2, y+1/2 INFO:: Found cif symmetry operator z+1, -x+1, -y+1/2 INFO:: Found cif symmetry operator -z+1, -x+1/2, y+1 INFO:: Found cif symmetry operator -z+1/2, x+1, -y+1 INFO:: Found cif symmetry operator y+1/2, z+1/2, x+1/2 INFO:: Found cif symmetry operator -y+1/2, z+1, -x+1 INFO:: Found cif symmetry operator y+1, -z+1, -x+1/2 INFO:: Found cif symmetry operator -y+1, -z+1/2, x+1 INFO:: space_group from symm ops in cif: I 21 3 import_hkl_info read 16736 hkls 16736 calculated data read on close_read() Read 16735 from CIF file (sigmaa). sigmaa and scaling... initializing map...done. doing fft...done. Mean and sigma of map from CIF file (make_map_from_cif): -1.00621e-05 and 0.046808 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 INFO:: spacegroup: I 21 3 Entered testcase - Write an INS from PDB test WARNING:: invalid molecule (204050) for write_shelx_ins_file ERROR transfering afix back WARNING:: failed to get AFIX handle for  ASP N , WARNING:: failed to get AFIX handle for  ASP CA , WARNING:: failed to get AFIX handle for  ASP CB , WARNING:: failed to get AFIX handle for  ASP CG , WARNING:: failed to get AFIX handle for  ASP OD1 , WARNING:: failed to get AFIX handle for  ASP OD2 , WARNING:: failed to get AFIX handle for  ASP C , WARNING:: failed to get AFIX handle for  ASP O , WARNING:: failed to get AFIX handle for  VAL N , WARNING:: failed to get AFIX handle for  VAL CA , INFO:: SHELXL file rnase.ins written. Entered testcase - new molecule by atom selection inherits shelx molecule flag In new_molecule_by_atom_selection has contains chain id B Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) Entered testcase - Addition of Terminal Residue on SHELX molecule has correct occupancy In new_molecule_by_atom_selection has contains chain id B Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) INFO:: Masking around 32 atoms fitting terminal residue with rigid body refinement using 100 trials INFO:: Fitting terminal residue with individual rigid body fitting. INFO:: found better residue, score: 1.66482 INFO:: found better residue, score: 2.99274 INFO:: found better residue, score: 4.17734 INFO:: found better residue, score: 5.3028 INFO:: found better residue, score: 5.32311 INFO:: found better residue, score: 6.70159 B 2021 ALA N :: xyz = ( -10.65, 18.09, 60.91) B 2021 ALA C :: xyz = ( -8.829, 18.52, 62.51) B 2021 ALA CA :: xyz = ( -10.33, 18.6, 62.24) B 2021 ALA O :: xyz = ( -8.235, 19.47, 63.03) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/atom_selection_from_insulin.res_Thu_Sep_10_12:19:40_2009_modification_0.res ERROR transfering afix back WARNING:: failed to get AFIX handle for Ú HIS N , WARNING:: failed to get AFIX handle for Ú HIS CA , WARNING:: failed to get AFIX handle for Ú HIS C , WARNING:: failed to get AFIX handle for Ú HIS O , WARNING:: failed to get AFIX handle for Ú HIS CB , WARNING:: failed to get AFIX handle for Ú HIS CG , WARNING:: failed to get AFIX handle for Ú HIS ND1 , WARNING:: failed to get AFIX handle for Ú HIS CE1 , WARNING:: failed to get AFIX handle for Ú HIS NE2 , WARNING:: failed to get AFIX handle for Ú HIS CD2 , DEBUG:: insert_coords_internal() add residue 0 of 4 1/B/2020/GLY/ N altLoc :: segid :: pos: (-9.63515,16.2417,57.4359) B-factor: 16.1806 1 of 4 1/B/2020/GLY/ CA altLoc :: segid :: pos: (-10.681,17.2571,57.2255) B-factor: 20.069 2 of 4 1/B/2020/GLY/ C altLoc :: segid :: pos: (-10.6427,18.37,58.2259) B-factor: 21.6855 3 of 4 1/B/2020/GLY/ O altLoc :: segid :: pos: (-9.56854,18.8859,58.5732) B-factor: 20.832 (add-terminal-residue 66 "B" 2020 1) Entered testcase - Add water to SHELX molecule (set-rotation-centre 3 -1 60) INFO:: adding atom of type Water at (3,-1,60) INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_insulin.res_Thu_Sep_10_12:19:40_2009_modification_0.res INFO :: padding UNIT card from size 5 to 5 1/D/3069/HOH/ O altLoc :: segid :: pos: (3,-1,60) B-factor: 45 added to molecule (place-typed-atom-at-pointer "Water") (resname-from-serial-number 62 "D" 68) (setnum-from-serial-number 62 "D" 68) (insertion-code-from-serial-number 62 "D" 68) Entered testcase - Find Waters for a SHELXL molecule (n-chains 62) Protein centre at: xyz = ( -0.2998, 10.6, 57.56) using sigma cut off 0.6 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.305067 INFO:: Using density cut-off: 0.18304 (0.6 sigma) (mean -0.0203646 stdev: 0.112003) INFO:: Using water to protein distance limits: 2.2 3.4 Finding clusters...done ------------------------------------------------------------- INFO:: cluster at xyz = ( -4.85, 20.81, 69.67) is too big to be water INFO:: cluster at xyz = ( 0.0273, 16.3, 69.67) is too big to be water INFO:: cluster at xyz = ( -4.576, 10.3, 69.42) is too big to be water INFO:: cluster at xyz = ( 15.6, 8.133, 53.54) is too big to be water INFO:: cluster at xyz = ( 20.54, 4.889, 65.84) is too big to be water WARNING:: refinement failure start pos: xyz = ( 7.187, 17.29, 73.17) final pos: xyz = ( 7.957, 17.95, 73.23) WARNING:: refinement failure start pos: xyz = ( 7.187, 17.29, 73.17) final pos: xyz = ( 7.957, 17.95, 73.23) WARNING:: refinement failure start pos: xyz = ( 7.187, 17.29, 73.17) final pos: xyz = ( 7.957, 17.95, 73.23) INFO:: found 58 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 0 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_insulin.res_Thu_Sep_10_12:19:40_2009_modification_1.res ERROR transfering afix back INFO :: padding UNIT card from size 5 to 5 WARNING:: failed to get AFIX handle for ý HOH O , INFO:: Adding to solvent chain: D (n-chains 62) (resname-from-serial-number 62 "D" 126) (setnum-from-serial-number 62 "D" 126) (insertion-code-from-serial-number 62 "D" 126) Entered testcase - NPD Anisotropic Atom [Mitch Miller] (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/miller/shelx-test4-NPD-mini.res" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O S SE CL WARNING:: BAD ATOM line 17 2 field(s) :DAMP 0.3: INFO:: CELL set to 42.14 83.03 89.79 90 90 90 INFO:: set space group to :P 21 21 21: READ-INS:: Spacegroup: P 21 21 21 INFO:: chain has 4 residues Symmetry available for this molecule Molecule 67 read successfully (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/miller/shelx-test4-NPD-mini.res") (close-molecule 67) Entered testcase - close shelx molecules (close-molecule 63) (close-molecule 62) Entered testcase - Aniso Bs in P21 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/horma-p21.res" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 INFO:: set space group to :P 1 21 1: READ-INS:: Spacegroup: P 1 21 1 INFO:: chain has 22 residues Symmetry available for this molecule Molecule 68 read successfully (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/horma-p21.res") INFO :: padding UNIT card from size 6 to 6 INFO:: SHELXL file new-horma.ins written. (handle-read-draw-molecule-with-recentre "new-horma.ins" 1) LATT LINE: LATT -1 SFAC LINE: SFAC C H N O MG CL INFO:: CELL set to 14.08 32.76 18.66 90 101.73 90 INFO:: set space group to :P 1 21 1: READ-INS:: Spacegroup: P 1 21 1 INFO:: chain has 22 residues Symmetry available for this molecule Molecule 69 read successfully (read-shelx-ins-file "new-horma.ins") b-1: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) b-2: (3.50660848617554 0.0295678526163101 0.0602300018072128 0.043437298387289 5.61549968551844e-4 -0.00681614130735397 -0.0034269078169018) Ended 02-shelx.scm Running 03-ligand.scm ... Entered testcase - Get monomer test /usr/bin/libcheck passing libcheck these data lines: ("N" "MON 3GP" "") /usr/bin/libcheck : : --- LIBCHECK --- /Vers 4.2.8 ; 02.06.2009/ : : : Do you want to have FILE-DOCUMENT /libcheck.doc/ ? //Y/A : : N - means without DOC-file : Y - with new contents : A - means to keep old contents and add new information : with DOC-file program creates batch file: libcheck.bat : _DOC: : : # : # Keywords: : # : #FILE_L: < > - additional library, " " means without this file : #MON: < > - give info about this monomer : # if = * , give list all monomers in the library : #FILE_PDB: < > - input PDB_file ," " means without this file : #FILE_SMILE: < > - input SMILE_file ," " means without this fil e : #FILE_SDF: < > - input SDF file, " " means without this file : #FILE_MOL: < > - input MOL file, " " means without this file : # use keyword MON as compound_id : #FILE_CIF: < > - input CIFile ," " means without this file : #FILE_CSD: < > - input CSD CIFile," " means without this file : #HFLAG: /A/N - Y - hydrogen atoms where they are : # A - with all hydrogen atoms : # N - without hydrogen atoms : #IND: /Y - Y - create index of mon_lib.cif : # output file: "new_mon_lib_ind.cif" : #FILE_O: - output files /library,coords,ps/, name without : # extention : #FILE_L2: < > - additional library (FILE_L) will be added to this library : # in this case program performs only adding : #ANGLE: <0.0> - rotation angle for picture ( around X ) : #LIST: /S/L - S short output, L - long, M - medium : #REF: /S,N,0 - 0 no refinement of new monomer : # N only crd->ang and ang->crd : # S plus torsion ref, Y plus restr.ref : # : #TEST: <0> - for program testing only : #COOR: /Y - use Vobs from coords instead Videal : #LCOOR: /N - Y use coords from lib description : #NODIST: /Y - Y not read the distributed library : # (only with FILE_L) : #SRCH: /Y/0 - Y - global search, 0 - for MON from PDB_file : # (only with NODIST = N) : : #--- type "keyword parameters" and/or --- : #--- press key "CR" to run program --- : --> --> MON : 3GP : ------------- : ------------- : Keywords: : HFLAG : Y : COOR : N : LCOOR : Y : SRCH : N : REF : Y : NODIST: N : ------------------------------ : --- LIBRARY OF MONOMERS --- : _lib_name mon_lib : _lib_version 4.16 : _lib_update 29/09/08 : ------------------------------ : NUMBER OF MONOMERS IN THE LIBRARY : 2445 : with complete description : 464 : NUMBER OF MODIFICATIONS : 48 : NUMBER OF LINKS : 64 : I am reading libraries. Please wait. : - energy parameters : - monomer"s description (links & mod ) : I am reading library. Please wait. : - monomer"s description : * CIFile : libcheck_3GP.cif : * PDBfile : libcheck_3GP.pdb : * Plotfile: libcheck_3GP.ps : I am writing new description to : file: libcheck.lib exit status: 0 INFO:: libcheck status: 0 /usr/bin/refmac5 : : :
: : :
: 
: ###############################################################
: ###############################################################
: ###############################################################
: ### CCP4 6.1: Refmac_5.5.0102     version 5.5.0102 : 07/07/09##
: ###############################################################
: User: unknown  Run date: 10/ 9/2009 Run time: 12:19:51 
:
:
: Please reference: Collaborative Computational Project, Number 4. 1994.
: "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
: as well as any specific reference in the program write-up.
:
:
: $TEXT:Reference1: $$ comment $$ 
:   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
:   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
:   Acta Crystallogr. D53, 240-255
:   EU  Validation contract: BIO2CT-92-0524
:
: $$
: $SUMMARY :Reference1:  $$ Refmac: $$
: :TEXT:Reference1: $$
:
:  Data line--- MODE NEWENTRY
:  Data line--- END
:===> Warning: Reflections file has not been defined
:===> Warning: Switching to the idealisation mode
: 
:    ****           Input and Default parameters#            ****
: 
: 
:Input coordinate file.  Logical name - XYZIN actual file name  - libcheck_3GP.pdb
:Output coordinate file. Logical name - XYZOUT actual file name - monomer-3GP.pdb
: 
:  Refinement type                        : Idealisation
: 
: 
:    ****                 Makecif parameters                 ****
: 
:Dictionary files for restraints : /usr/share/ccp4/data/monomers/mon*cif
:Parameters for new entry and VDW: /usr/share/ccp4/data/monomers/ener_lib.cif
:User supplied dictionary entries: libcheck_3GP.cif
:    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
:    Hydrogens will be restored in their riding positions
:    hydrogens will be written to the output file
:    Links between monomers will be checked. Only those links present in the coordinate file will be used
:    Standard sugar links will be analysed and used
:    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
:    Symmetry related links will be analysed and used
:    Cis peptides will be found and used automatically
: 
: 
: 
: 
:Monitoring style is "MEDIUM". Complete information will be printed out in the
:first and last cycle. In all other cycles minimum information will be printed out
:Sigma cutoffs for printing out outliers
:If deviation of restraint parameter > alpha*sigma then information will be printed out
:Distance outliers      10.000
:Angle outliers         10.000
:Torsion outliers       10.000
:Chiral volume outliers 10.000
:Plane outliers         10.000
:Non-bonding outliers   10.000
:---------------------------------------------------------------
: 
: Input file :libcheck_3GP.pdb
:  ------------------------------
:  ---  LIBRARY OF MONOMERS   ---
: _lib_name         mon_lib
: _lib_version      4.16
: _lib_update       29/09/08
:  ------------------------------
:  NUMBER OF MONOMERS IN THE LIBRARY          :  2445
:                with complete description    :   464
:  NUMBER OF MODIFICATIONS                    :    48
:  NUMBER OF LINKS                            :    64
:  I am reading libraries. Please wait.
:      - energy parameters
:      - monomer"s description (links & mod )
:
:FORMATTED      OLD     file opened on unit  45
:
:Logical name: ATOMSF, Filename: /usr/share/ccp4/data/atomsf.lib
:
:
: CRYST1  100.000  100.000  100.000  90.00  90.00  90.00 P 1
:
: Spacegroup information obtained from library file: 
: Logical Name: SYMINFO   Filename: /usr/share/ccp4/data/syminfo.lib
:
:  WARNING: "SCALE" card is absent in input PDB file
:  Number of atoms    :      36
:  Number of residues :       1
:  Number of chains   :       1
:  I am reading library. Please wait.
:                mon_lib.cif
:  --------------------------------
:  --- title of input coord file ---
:
:  PDB_code:3GP
:  PDB_name:coords of 3GP from prog: libcheck
:  PDB_date:XX-XXX-XX
:  --------------------------------
:  Number of chains                  :       1
:  Total number of monomers          :       1
:  Number of atoms                   :      36
:  Number of missing atoms           :       0
:  Number of rebuilt atoms           :       0
:  Number of unknown atoms           :       0
:  Number of deleted atoms           :       0
:Substructure refinement not activated.
: 
: 
: loop_
:     _atom_type_symbol
:     _atom_type_scat_Cromer_Mann_a1
:     _atom_type_scat_Cromer_Mann_b1
:     _atom_type_scat_Cromer_Mann_a2
:     _atom_type_scat_Cromer_Mann_b2
:     _atom_type_scat_Cromer_Mann_a3
:     _atom_type_scat_Cromer_Mann_b3
:     _atom_type_scat_Cromer_Mann_a4
:     _atom_type_scat_Cromer_Mann_b4
:     _atom_type_scat_Cromer_Mann_c
: 
: 
:  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
:  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
:  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
:  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
:  P      6.4345   1.9067   4.1791  27.1570   1.7800   0.5260   1.4908  68.1645   1.1149
: 
: 
: Bonds before and after          38          38
: Angles before and after          66          66
: Chirals before and after           4           4
: planes before and after           1           1
: Torsions before and after          25          25
: 
: 
:     CGMAT cycle number =      1
: 
:    ****      Large deviation of atoms from planarity       ****
: 
:Deviations from the planarity >10.000Sigma will be monitored
:Atom: A      1 3GP H8    deviation=  -0.24 sigma.=   0.02
: 
: function value    11172.728    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.014     0.020
:Bond distances: others                           12     0.001     0.020
:Bond angles  : refined atoms                     40     4.506     3.000
:Bond angles  : others                            26     2.878     3.000
:Chiral centres: refined atoms                     4     0.382     0.200
:Planar groups: refined atoms                     12     0.070     0.020
:Planar groups: others                             2     0.168     0.020
:VDW repulsions: refined_atoms                     1     0.062     0.200
:VDW repulsions.others                             7     0.442     0.200
:VDW; torsion: refined_atoms                       7     0.269     0.200
:VDW; torsion.others                               5     0.250     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
: 
: 
: 
: 
:     CGMAT cycle number =      2
: 
: function value    569.45349    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.079     0.020
:Bond distances: others                           12     0.113     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
: 
: 
: 
: 
: 
:     CGMAT cycle number =      3
: 
: function value    513.53339    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.078     0.020
:Bond distances: others                           12     0.086     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
: 
: 
: 
: 
:     CGMAT cycle number =      4
: 
: function value    299.73331    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.076     0.020
:Bond distances: others                           12     0.012     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Gamma decreased to   1.66446287E-02
: 
: 
: 
: 
: 
:     CGMAT cycle number =      5
: 
: function value    304.48044    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.009     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   1.66446287E-02
: Gamma decreased to   9.13148094E-03
: 
: 
: 
: 
: 
:     CGMAT cycle number =      6
: 
: function value    281.81296    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.008     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   9.13148094E-03
: Gamma decreased to   2.30134674E-03
: 
: 
: 
: 
: 
:     CGMAT cycle number =      7
: 
: function value    307.33380    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.007     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.30134674E-03
: Not converging with gamma equal   2.30134674E-03
: Trying gamma equal   3.64520177E-02
: Gamma decreased to   2.96218842E-02
: 
: 
: 
: 
: 
:     CGMAT cycle number =      8
: 
: function value    290.29788    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.96218842E-02
: Gamma decreased to   2.34126709E-02
: 
: 
: 
: 
:     CGMAT cycle number =      9
: 
: function value    243.62866    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.34126709E-02
: Gamma decreased to   1.77679323E-02
: 
: 
: 
: 
: 
:     CGMAT cycle number =     10
: 
: function value    277.06702    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   1.77679323E-02
: Gamma decreased to   1.26363514E-02
: 
: 
: 
: 
:     CGMAT cycle number =     11
: 
: function value    241.62645    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.002     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   1.26363514E-02
: Gamma decreased to   7.97127839E-03
: 
: 
: 
: 
:     CGMAT cycle number =     12
: 
: function value    240.87976    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.002     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.97127839E-03
: Gamma decreased to   3.73030291E-03
: 
: 
: 
: 
:     CGMAT cycle number =     13
: 
: function value    240.21413    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.002     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.73030291E-03
: Gamma decreased to    0.0000000    
: 
: 
: 
: 
: 
:     CGMAT cycle number =      1
: 
: function value    3416.9084    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.075     0.020
:Bond distances: others                           12     0.002     0.020
:Bond angles  : refined atoms                     40     3.454     3.000
:Bond angles  : others                            26     2.005     3.000
:Chiral centres: refined atoms                     4     0.074     0.200
:Planar groups: refined atoms                     12     0.002     0.020
:Planar groups: others                             2     0.004     0.020
:VDW repulsions.others                             8     0.001     0.200
:VDW; torsion: refined_atoms                       5     0.030     0.200
:VDW; torsion.others                               3     0.002     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
: 
: 
: 
: 
:     CGMAT cycle number =      2
: 
: function value    599.91724    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.070     0.020
:Bond distances: others                           12     0.011     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
: 
: 
: 
: 
:     CGMAT cycle number =      3
: 
: function value    461.69443    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.058     0.020
:Bond distances: others                           12     0.005     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Gamma decreased to   2.49090921E-02
: 
: 
: 
: 
:     CGMAT cycle number =      4
: 
: function value    416.44482    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.051     0.020
:Bond distances: others                           12     0.004     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   2.49090921E-02
: Not converging with gamma equal   2.49090921E-02
: Trying gamma equal   7.03636408E-02
: Gamma decreased to   6.12727329E-02
: 
: 
: 
: 
:     CGMAT cycle number =      5
: 
: function value    401.89377    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.048     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.12727329E-02
: Not converging with gamma equal   6.12727329E-02
: Trying gamma equal   0.10672728    
: Not converging with gamma equal   0.10672728    
: Trying gamma equal   0.15672728    
: Not converging with gamma equal   0.15672728    
: Trying gamma equal   0.21172729    
: Gamma decreased to   0.20072728    
: 
: 
: 
: 
:     CGMAT cycle number =      6
: 
: function value    397.19699    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.047     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.20072728    
: Gamma decreased to   0.19072728    
: 
: 
: 
: 
:     CGMAT cycle number =      7
: 
: function value    392.69656    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.046     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.19072728    
: Gamma decreased to   0.18163636    
: 
: 
: 
: 
:     CGMAT cycle number =      8
: 
: function value    388.36441    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.045     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.18163636    
: Gamma decreased to   0.17337190    
: 
: 
: 
: 
:     CGMAT cycle number =      9
: 
: function value    384.18506    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.044     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.17337190    
: Gamma decreased to   0.16585875    
: 
: 
: 
: 
:     CGMAT cycle number =     10
: 
: function value    380.14911    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.043     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.16585875    
: Gamma decreased to   0.15902860    
: 
: 
: 
: 
:     CGMAT cycle number =     11
: 
: function value    376.24887    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.042     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15902860    
: Gamma decreased to   0.15281940    
: 
: 
: 
: 
:     CGMAT cycle number =     12
: 
: function value    372.48080    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.15281940    
: Gamma decreased to   0.14717466    
: 
: 
: 
: 
:     CGMAT cycle number =     13
: 
: function value    368.84195    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.041     0.020
:Bond distances: others                           12     0.003     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   0.14717466    
: Gamma decreased to   0.14204307    
: 
: 
: 
: 
:     CGMAT cycle number =      1
: 
: function value    71.200081    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.040     0.020
:Bond distances: others                           12     0.003     0.020
:Bond angles  : refined atoms                     40     1.088     3.000
:Bond angles  : others                            26     0.484     3.000
:Chiral centres: refined atoms                     4     0.172     0.200
:Planar groups: refined atoms                     12     0.010     0.020
:Planar groups: others                             2     0.002     0.020
:VDW repulsions.others                             9     0.236     0.200
:VDW; torsion: refined_atoms                       6     0.264     0.200
:VDW; torsion.others                               6     0.095     0.200
:-------------------------------------------------------------------------------
: Trying gamma equal    0.0000000    
: Not converging with gamma equal    0.0000000    
: Trying gamma equal   5.50000034E-02
: Gamma decreased to   4.40000035E-02
: 
: 
: 
: 
:     CGMAT cycle number =      2
: 
: function value    19.325279    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.009     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   4.40000035E-02
: Gamma decreased to   3.40000018E-02
: 
: 
: 
: 
:     CGMAT cycle number =      3
: 
: function value    16.832470    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.005     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   3.40000018E-02
: Not converging with gamma equal   3.40000018E-02
: Trying gamma equal   8.40000063E-02
: Gamma decreased to   7.40000084E-02
: 
: 
: 
: 
:     CGMAT cycle number =      4
: 
: function value    16.460804    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.005     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.40000084E-02
: Gamma decreased to   6.49091005E-02
: 
: 
: 
: 
:     CGMAT cycle number =      5
: 
: function value    16.247694    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.004     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.49091005E-02
: Gamma decreased to   5.66446371E-02
: 
: 
: 
: 
:     CGMAT cycle number =      6
: 
: function value    16.092873    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.004     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.66446371E-02
: Not converging with gamma equal   5.66446371E-02
: Trying gamma equal   9.79669541E-02
: Gamma decreased to   8.97024944E-02
: 
: 
: 
: 
:     CGMAT cycle number =      7
: 
: function value    16.009205    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.004     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   8.97024944E-02
: Gamma decreased to   8.21893439E-02
: 
: 
: 
: 
:     CGMAT cycle number =      8
: 
: function value    15.931965    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.004     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   8.21893439E-02
: Gamma decreased to   7.53592104E-02
: 
: 
: 
: 
:     CGMAT cycle number =      9
: 
: function value    15.858668    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.004     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   7.53592104E-02
: Gamma decreased to   6.91500008E-02
: 
: 
: 
: 
:     CGMAT cycle number =     10
: 
: function value    15.787797    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.003     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.91500008E-02
: Gamma decreased to   6.35052621E-02
: 
: 
: 
: 
:     CGMAT cycle number =     11
: 
: function value    15.718227    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.003     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   6.35052621E-02
: Gamma decreased to   5.83736822E-02
: 
: 
: 
: 
:     CGMAT cycle number =     12
: 
: function value    15.649114    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.003     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.83736822E-02
: Gamma decreased to   5.37086092E-02
: 
: 
: 
: 
:     CGMAT cycle number =     13
: 
: function value    15.579708    
: 
:-------------------------------------------------------------------------------
:             Restraint type              N restraints   Rms Delta   Av(Sigma)
:Bond distances: refined atoms                    26     0.003     0.020
:Bond distances: others                           12     0.001     0.020
:-------------------------------------------------------------------------------
: Trying gamma equal   5.37086092E-02
: Not converging with gamma equal   5.37086092E-02
: Trying gamma equal   7.70339742E-02
: Gamma decreased to   7.23689049E-02
: 
: 
:  Time in seconds: CPU =         2.09
:             Elapsed =           5.00
: 
:    **** Things for loggraph, R factor and others vs cycle  ****
: 
: 
:$TABLE: Rfactor analysis, stats vs cycle  :
:$GRAPHS: vs cycle :N:1,2,3:
::FOM vs cycle :N:1,4:
::-LL vs cycle :N:1,5:
::-LLfree vs cycle :N:1,6:
::Geometry vs cycle:N:1,7,8,9,10,11:
:$$
:    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
:$$
: $$
: $TEXT:Result: $$ Final results $$
: $$
: Harvest: NO PNAME_KEYWRD given - no deposit file created
:
: Refmac_5.5.0102:  End of Refmac_5.5.0102 
:Times: User:       7.4s System:    1.7s Elapsed:     0:16  
:
: : exit status: 0 DEBUG:: libcheck-minimal? returns #f (handle-read-draw-molecule-with-recentre "monomer-3GP.pdb" 0) Reading coordinate file: monomer-3GP.pdb PDB file monomer-3GP.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 70 read successfully (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) INFO:: backup file coot-backup/monomer-3GP.pdb_Thu_Sep_10_12:20:07_2009_modification_0.pdb.gz There are 2 data in libcheck_3GP.cif Read 36 atoms/links in restraints from libcheck_3GP.cif INFO:: backup file coot-backup/monomer-3GP.pdb_Thu_Sep_10_12:20:07_2009_modification_1.pdb.gz (delete-residue-hydrogens 70 "A" 1 "" "") Entered testcase - Set Bond thickness Entered testcase - Move and Refine Ligand test (go-to-view-number 2 1) (set-rotation-centre 55.3 9.1 20.6) (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) INFO:: backup file coot-backup/monomer-3GP.pdb_Thu_Sep_10_12:20:07_2009_modification_2.pdb.gz (backup-state 70) (turn-off-backup 70) No graphics! Can't make Map Selection dialog. ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... (turn-on-backup 70) Entered testcase - Many Molecules - Ligand Fitting (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb" 0) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 71 read successfully Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 71) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 71) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 71) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 71) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 71) (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb has been read. Spacegroup: C 2 2 21 Cell: 106.25 110.86 244.42 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 107/113 INFO:: NCS chain comparison 10/113 INFO:: NCS chain comparison 0/113 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 10/117 INFO:: NCS chain comparison 112/117 INFO:: NCS chain comparison 0/117 INFO:: fill_ghost_info Constructed 6 ghosts Ghost 0 name: "NCS found from matching Chain C onto Chain A" Ghost 1 name: "NCS found from matching Chain E onto Chain A" Ghost 2 name: "NCS found from matching Chain G onto Chain A" Ghost 3 name: "NCS found from matching Chain D onto Chain B" Ghost 4 name: "NCS found from matching Chain F onto Chain B" Ghost 5 name: "NCS found from matching Chain H onto Chain B" Molecule 77 read successfully making conventional map from MTZ filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using FWT PHWT Number of OBSERVED reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.61 seconds to read MTZ file INFO:: 0.797 seconds to initialize map INFO:: 0.602 seconds for FFT INFO:: 0.158 seconds for statistics Map mean: ........ -8.79074e-07 Map sigma: ....... 0.171188 Map maximum: ..... 1.34304 Map minimum: ..... -0.695441 INFO:: 0.017 seconds for contour map INFO:: 2.184 seconds in total (make-and-draw-map-with-reso-with-refmac-params "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) making difference map from MTZ filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz using DELFWT PHDELWT Number of OBSERVED reflections: 54440 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 160, 160, 336) INFO:: 0.34 seconds to read MTZ file INFO:: 0.024 seconds to initialize map INFO:: 0.478 seconds for FFT INFO:: 0.177 seconds for statistics Map mean: ........ 2.0939e-06 Map sigma: ....... 0.0333923 Map maximum: ..... 0.366077 Map minimum: ..... -0.191665 INFO:: 0.008 seconds for contour map INFO:: 1.027 seconds in total (make-and-draw-map-with-reso-with-refmac-params "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz" "DELFWT" "PHDELWT" "" 0 1 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) Executing ligand search... INFO:: ligand number 0 is molecule number 71 with wiggly flag: 0 Protein centre at: xyz = ( 58.29, 34.65, 30.63) Map statistics: mean: -0.0216745 st.d: 0.0886263 Map statistics: min: -0.695441, max: 0.754209 -0.6592 14 -0.586717 143 -0.514235 1331 -0.441752 5299 -0.36927 11732 -0.296787 16725 -0.224305 21484 -0.151822 46755 -0.0793395 161103 -0.006857 614774 0.0656255 162933 0.138108 28508 0.210591 3055 0.283073 813 0.355556 334 0.428038 197 0.500521 78 0.573003 48 0.645486 25 0.717968 9 0.790451 0 INFO:: find_clusters map_rms is 0.171188 INFO:: Using density cut-off: 0.171188 (1 sigma) (mean -0.0216776 stdev: 0.0886191) INFO:: Using water to protein distance limits: 2.4 3.2 Finding clusters...done WARNING: many badly fitting atoms for best ligand in cluster 4. Coordinates not written. Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Symmetry available for this molecule Fitting NPO gave these results: (81 82 83 84 85 86 87 88 89 90) Entered testcase - flip residue (around eigen vectors) (handle-read-draw-molecule-with-recentre "monomer-3GP.pdb" 1) Reading coordinate file: monomer-3GP.pdb PDB file monomer-3GP.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 91 read successfully Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 91) INFO:: backup file coot-backup/Copy_of_monomer-3GP.pdb_Thu_Sep_10_12:20:22_2009_modification_0.pdb.gz INFO:: replace_coords: 36 atoms updated. distance: 4.70367229880093 INFO:: backup file coot-backup/Copy_of_monomer-3GP.pdb_Thu_Sep_10_12:20:22_2009_modification_1.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_monomer-3GP.pdb_Thu_Sep_10_12:20:22_2009_modification_2.pdb.gz INFO:: replace_coords: 36 atoms updated. INFO:: backup file coot-backup/Copy_of_monomer-3GP.pdb_Thu_Sep_10_12:20:22_2009_modification_3.pdb.gz INFO:: replace_coords: 36 atoms updated. distance d2: 2.73979842784955e-7 Entered testcase - Test dipole (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/dipole-residues.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/dipole-residues.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/dipole-residues.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 93 read successfully info:: dipole components (-2.21999993920326 3.6949610038306e-16 -4.61870125478825e-17) Entered testcase - Reading new dictionary replaces WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_3GP.cif not found. init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_3GP.cif not found. init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_3GP.cif had no bond restraints WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_3GP.cif not found. init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_3GP.cif had no bond restraints Ended 03-ligand.scm Running 04-cootaneer.scm ... Entered testcase - Assignment of new PIR sequence overwrites old assignment (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 94 read successfully in assign_pir_sequence storing sequence: ACDEFGHIKLMNPQ for chain id: A (assign-pir-sequence "A" ">test ACDEFGHIKLMNPQ*") debug seq: ("A" . "ACDEFGHIKLMNPQ") in assign_pir_sequence storing sequence: ACDEFGHIKLMNPQRST for chain id: A (assign-pir-sequence "A" ">test ACDEFGHIKLMNPQRST*") Entered testcase - Cootaneer Beta Strand (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/crashes_on_cootaneering.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/crashes_on_cootaneering.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/crashes_on_cootaneering.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 2/2 INFO:: NCS chain comparison 0/2 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain A onto Chain " Molecule 95 read successfully (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.054 seconds to read MTZ file INFO:: 0.001 seconds to initialize map INFO:: 0.081 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.057 seconds for contour map INFO:: 0.202 seconds in total in assign_pir_sequence storing sequence: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID for chain id: A (assign-pir-sequence "A" "> tutorial-modern chain A RNASE DVSGTVCLSA LPPEATDTLN LIASDGPFPY SQDGVVFQNR ESVLPTQSYG YYHEYTVITP GARTRGTRRI ICGEATQEDY YTGDHYATFS LID * ") (set-rotation-centre 64.271 7.036 14.42) Cootaneering: imol 95 chain-id "B" resno 60 inscode "" at-name " CA " alt-conf "" Ooops! Can't find cootaneer likelihood data! - failure Ended 04-cootaneer.scm Running 05-rna-ghosts.scm ... Entered testcase - RNA NCS Ghosts INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0 max devi: 0 min devi: 0 request std_res of type Gr and got Gr coot::util::mutate_base Gr with std Gr INFO:: 5 matched atoms had: mean devi: 0.0120681 rms devi: 0.0134464 max devi: 0.0214179 min devi: 0.00385596 request std_res of type Ar and got Ar coot::util::mutate_base Ar with std Ar INFO:: 5 matched atoms had: mean devi: 0.270216 rms devi: 0.335002 max devi: 0.536002 min devi: 0.08463 request std_res of type Cr and got Cr coot::util::mutate_base Cr with std Cr INFO:: 5 matched atoms had: mean devi: 0.26738 rms devi: 0.322791 max devi: 0.495136 min devi: 0.112289 request std_res of type Ur and got Ur coot::util::mutate_base Ur with std Ur INFO:: 5 matched atoms had: mean devi: 0.270247 rms devi: 0.335033 max devi: 0.536044 min devi: 0.0847029 request std_res of type Cr and got Cr coot::util::mutate_base Cr with std Cr INFO:: 5 matched atoms had: mean devi: 0.267411 rms devi: 0.322823 max devi: 0.495177 min devi: 0.112221 request std_res of type Ur and got Ur coot::util::mutate_base Ur with std Ur INFO:: 5 matched atoms had: mean devi: 0.011982 rms devi: 0.013349 max devi: 0.0212578 min devi: 0.0038732 request std_res of type Ar and got Ar coot::util::mutate_base Ar with std Ar INFO:: 5 matched atoms had: mean devi: 0.000242576 rms devi: 0.000242751 max devi: 0.000256671 min devi: 0.000231275 request std_res of type Gr and got Gr coot::util::mutate_base Gr with std Gr INFO:: 5 matched atoms had: mean devi: 0.270185 rms devi: 0.334971 max devi: 0.535961 min devi: 0.0845571 request std_res of type Cr and got Cr coot::util::mutate_base Cr with std Cr INFO:: 5 matched atoms had: mean devi: 0.267349 rms devi: 0.322759 max devi: 0.495094 min devi: 0.112357 request std_res of type Ur and got Ur coot::util::mutate_base Ur with std Ur INFO:: 5 matched atoms had: mean devi: 6.9313e-05 rms devi: 6.93629e-05 max devi: 7.33402e-05 min devi: 6.60841e-05 request std_res of type Gr and got Gr coot::util::mutate_base Gr with std Gr INFO:: 5 matched atoms had: mean devi: 0.0120334 rms devi: 0.0134072 max devi: 0.0213538 min devi: 0.00386188 request std_res of type Ar and got Ar coot::util::mutate_base Ar with std Ar INFO:: 5 matched atoms had: mean devi: 0.000138622 rms devi: 0.000138721 max devi: 0.000146676 min devi: 0.000132164 request std_res of type Gr and got Gr coot::util::mutate_base Gr with std Gr INFO:: 5 matched atoms had: mean devi: 0.011999 rms devi: 0.0133684 max devi: 0.0212898 min devi: 0.0038691 request std_res of type Ar and got Ar coot::util::mutate_base Ar with std Ar INFO:: 5 matched atoms had: mean devi: 0.267426 rms devi: 0.322839 max devi: 0.495197 min devi: 0.112187 request std_res of type Ur and got Ur coot::util::mutate_base Ur with std Ur INFO:: 5 matched atoms had: mean devi: 0.270294 rms devi: 0.335079 max devi: 0.536106 min devi: 0.0848122 request std_res of type Cr and got Cr coot::util::mutate_base Cr with std Cr !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: backup file coot-backup/Ideal-A-form-RNA_Thu_Sep_10_12:20:25_2009_modification_0.pdb.gz (ideal-nucleic-acid "RNA" "A" 0 "GACUCUAG") !! Warning:: No symmetry available for this molecule No Symmetry for this model (update-go-to-atom-window-on-new-mol) (copy-molecule 97) (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) (set-rotation-centre 76.271 10.036 14.42) (go-to-view-number 3 1) (n-chains 98) (chain_id 98 0) (chain_id 98 1) (is-solvent-chain-p 98 "A") There are 8 residues in chain "A" (resname-from-serial-number 98 "A" 0) (setnum-from-serial-number 98 "A" 0) (insertion-code-from-serial-number 98 "A" 0) (resname-from-serial-number 98 "A" 1) (setnum-from-serial-number 98 "A" 1) (insertion-code-from-serial-number 98 "A" 1) (resname-from-serial-number 98 "A" 2) (setnum-from-serial-number 98 "A" 2) (insertion-code-from-serial-number 98 "A" 2) (resname-from-serial-number 98 "A" 3) (setnum-from-serial-number 98 "A" 3) (insertion-code-from-serial-number 98 "A" 3) (resname-from-serial-number 98 "A" 4) (setnum-from-serial-number 98 "A" 4) (insertion-code-from-serial-number 98 "A" 4) (resname-from-serial-number 98 "A" 5) (setnum-from-serial-number 98 "A" 5) (insertion-code-from-serial-number 98 "A" 5) (resname-from-serial-number 98 "A" 6) (setnum-from-serial-number 98 "A" 6) (insertion-code-from-serial-number 98 "A" 6) (resname-from-serial-number 98 "A" 7) (setnum-from-serial-number 98 "A" 7) (insertion-code-from-serial-number 98 "A" 7) (is-solvent-chain-p 98 "B") There are 8 residues in chain "B" (resname-from-serial-number 98 "B" 0) (setnum-from-serial-number 98 "B" 0) (insertion-code-from-serial-number 98 "B" 0) (resname-from-serial-number 98 "B" 1) (setnum-from-serial-number 98 "B" 1) (insertion-code-from-serial-number 98 "B" 1) (resname-from-serial-number 98 "B" 2) (setnum-from-serial-number 98 "B" 2) (insertion-code-from-serial-number 98 "B" 2) (resname-from-serial-number 98 "B" 3) (setnum-from-serial-number 98 "B" 3) (insertion-code-from-serial-number 98 "B" 3) (resname-from-serial-number 98 "B" 4) (setnum-from-serial-number 98 "B" 4) (insertion-code-from-serial-number 98 "B" 4) (resname-from-serial-number 98 "B" 5) (setnum-from-serial-number 98 "B" 5) (insertion-code-from-serial-number 98 "B" 5) (resname-from-serial-number 98 "B" 6) (setnum-from-serial-number 98 "B" 6) (insertion-code-from-serial-number 98 "B" 6) (resname-from-serial-number 98 "B" 7) (setnum-from-serial-number 98 "B" 7) (insertion-code-from-serial-number 98 "B" 7) finding new chain id for chain id :A: 0/2 finding new chain id for chain id :B: 1/2 INFO:: Merge From chains: :A: :B: INFO:: Merge To chains: :C: :D: !! Warning:: No symmetry available for this molecule No Symmetry for this model (update-go-to-atom-window-on-new-mol) (copy-molecule 97) INFO:: Matching/moving molecule number 99 to 99 INFO:: LSQ matched 125 atoms INFO:: 125 matched atoms had: mean devi: 0.141862 rms devi: 0.1486 max devi: 0.243102 min devi: 0.0283184 INFO:: Axis orientation: ( 0.3864, -0.6781, -0.6252) INFO:: Rotation in CCP4 Polar Angles: Polar = (128.694,-60.3226,0.295211) INFO:: backup file coot-backup/Copy_of_Ideal-A-form-RNA_Thu_Sep_10_12:20:26_2009_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 1, 0.003218, -0.003497| | -0.003225, 1, -0.001985| | 0.003491, 0.001997, 1| ( -24.02, -23.69, -24.44) No unit cell for this molecule, hence no fractional matrix. (close-molecule 99) (close-molecule 98) (go-to-view-number 4 1) Ended 05-rna-ghosts.scm Running 06-ssm.scm ... Entered testcase - SSM - Frank von Delft's Example (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1wly.pdb" 0) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1wly.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1wly.pdb has been read. Spacegroup: C 1 2 1 Cell: 140.797 49.176 59.053 90 100.97 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 100 read successfully (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1yb5.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1yb5.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1yb5.pdb has been read. Spacegroup: P 21 21 2 Cell: 99.484 110.239 77.253 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 324/324 INFO:: NCS chain comparison 0/324 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 101 read successfully do_Ca_plus_ligands_bonds with atom_colour_type 0 (graphics-to-ca-plus-ligands-representation 100) do_Ca_plus_ligands_bonds with atom_colour_type 0 (graphics-to-ca-plus-ligands-representation 101) INFO:: reference 100 has 750 atoms selected INFO:: moving 101 has 842 atoms selected superposing... number of Ca atoms in selections: 110 (moving) and 100 (reference) Another Go... Moving Reference Distance A 6 A 7 A 8 <---> A 2 : 37.9486 A A 9 <---> A 3 : 33.2896 A A 10 <---> A 4 : 29.0024 A A 11 <---> A 5 : 24.6904 A A 12 <---> A 6 : 28.5441 A A 13 <---> A 7 : 26.6907 A A 14 <---> A 8 : 32.2536 A A 15 <---> A 9 : 27.956 A A 16 <---> A 10 : 21.8523 A A 17 <---> A 11 : 15.8159 A A 18 <---> A 12 : 11.5358 A A 19 <---> A 13 : 12.169 A A 20 <---> A 14 : 18.9048 A A 21 <---> A 15 : 21.4067 A A 22 <---> A 16 : 21.2011 A A 23 <---> A 17 : 28.0666 A A 24 <---> A 18 : 29.6762 A A 25 <---> A 19 : 36.2328 A A 26 <---> A 20 : 40.0359 A A 27 A 28 <---> A 21 : 41.7249 A A 29 <---> A 22 : 46.7543 A A 30 A 31 <---> A 23 : 45.0273 A A 32 <---> A 25 : 51.5677 A A 33 <---> A 26 : 50.9334 A A 34 <---> A 27 : 57.2887 A A 35 <---> A 28 : 60.0078 A A 36 <---> A 29 : 54.9492 A A 37 <---> A 30 : 48.9269 A A 38 <---> A 31 : 43.7031 A A 39 <---> A 32 : 39.8913 A A 40 <---> A 33 : 32.5741 A A 41 <---> A 34 : 28.7099 A A 42 <---> A 35 : 22.3463 A A 43 <---> A 36 : 16.0517 A A 44 <---> A 37 : 11.3047 A A 45 <---> A 38 : 12.5393 A A 46 <---> A 39 : 11.2767 A A 47 <---> A 40 : 9.09777 A A 48 <---> A 41 : 14.2068 A A 49 <---> A 42 : 14.176 A A 50 <---> A 43 : 18.6314 A A 51 <---> A 44 : 15.3568 A A 52 <---> A 45 : 10.7864 A A 53 <---> A 46 : 15.706 A A 54 <---> A 47 : 20.1805 A A 55 <---> A 48 : 16.7407 A A 56 <---> A 49 : 14.2016 A A 57 A 58 A 59 A 60 A 61 A 62 A 63 A 64 A 65 <---> A 60 : 36.1129 A A 66 <---> A 61 : 36.1605 A A 67 <---> A 62 : 32.2488 A A 68 <---> A 63 : 27.9529 A A 69 <---> A 64 : 22.5019 A A 70 <---> A 65 : 20.5387 A A 71 <---> A 66 : 24.4775 A A 72 <---> A 67 : 20.9202 A A 73 <---> A 68 : 19.2174 A A 74 <---> A 69 : 18.4197 A A 75 <---> A 70 : 21.9936 A A 76 <---> A 71 : 26.7859 A A 77 <---> A 72 : 34.0449 A A 78 <---> A 73 : 37.3758 A A 79 <---> A 74 : 44.3688 A A 80 <---> A 75 : 48.335 A A 81 <---> A 76 : 54.5872 A A 82 <---> A 77 : 61.3581 A A 83 <---> A 78 : 61.274 A A 84 <---> A 79 : 53.9665 A A 85 <---> A 80 : 54.3481 A A 86 <---> A 81 : 49.1624 A A 87 <---> A 82 : 43.7062 A A 88 <---> A 83 : 42.4154 A A 89 <---> A 84 : 39.2673 A A 90 <---> A 85 : 32.0616 A A 91 <---> A 86 : 31.1771 A A 92 <---> A 87 : 25.2044 A A 93 <---> A 88 : 27.4312 A A 94 <---> A 89 : 25.4609 A A 95 <---> A 90 : 28.3928 A A 96 <---> A 91 : 29.1483 A A 97 <---> A 92 : 32.8561 A A 98 A 99 A 100 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_1yb5.pdb_Thu_Sep_10_12:20:28_2009_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.9117, -0.3803, 0.1557| | -0.3625, 0.9227, 0.131| | -0.1935, 0.06299, -0.9791| ( 70.65, 7.793, 21.29) Rotation - polar (omega,phi,kappa) 87.1413 101.022 169.739 Rotation - euler (alpha,beta,gamma) 40.0716 168.257 18.0277 Translation - Angstroms 70.6538 7.793 21.2852 do_Ca_plus_ligands_bonds with atom_colour_type 0 INFO: core rmsd achieved: 1.01989 Angstroems number of residues in reference structure: 322 number of residues in moving structure: 324 number of residues in aligned sections (reference): 100 number of residues in aligned sections (moving): 110 number of aligned residues: 95 number of gaps: 4 number of misdirections: 0 number of SSE combinations: 4 sequence identity: 30.5263% (set-rotation-centre 65.65 -3 -4) (go-to-view-number 5 1) Entered testcase - SSM - Alice Dawson's Example (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1pyd.pdb" 0) Error reading /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1pyd.pdb (graphics-to-ca-plus-ligands-representation -1) (set-graphics-window-size 687 452) (molecule-name 0) 0 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 1) 1 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/ins-code-fragment-pre.pdb" 2 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 3 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 4 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" 5 "test-3hfl.map" (molecule-name 6) 6 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb" (molecule-name 7) 7 "atom selection from tutorial-add-terminal-1-test.pdb" (molecule-name 8) 8 "sphere selection from tutorial-modern.pdb" (molecule-name 10) 10 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rotamer-test-fragment.pdb" (molecule-name 11) 11 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/res098.pdb" (molecule-name 12) 12 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-pepflip-test.pdb" (molecule-name 13) 13 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" (molecule-name 14) 14 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 15 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" (molecule-name 16) 16 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb" (molecule-name 17) 17 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-waters.pdb" (molecule-name 18) 18 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/backrub-fragment.pdb" (molecule-name 19) 19 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/backrub-fragment.pdb" (molecule-name 20) 20 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/coords-B3A.pdb" 21 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz /RNASE3GMP/COMPLEX/FWT /RNASE3GMP/COMPLEX/PHWT" (molecule-name 22) 22 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/test-TER-OXT.pdb" (molecule-name 23) 23 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/val.pdb" 24 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 25 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" (molecule-name 26) 26 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 27 "Generic Masked Map" 28 "difference-map" 29 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 30 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" 31 "averaged-map" 32 "difference-map" (molecule-name 33) 33 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/multi-carbo-coot-2.pdb" (molecule-name 34) 34 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-VAL.pdb" (molecule-name 35) 35 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3ins-6B-3.0.pdb" (molecule-name 36) 36 "atom selection from tutorial-modern.pdb" (molecule-name 37) 37 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-ACT.pdb" (molecule-name 38) 38 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 39) 39 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 40) 40 "atom selection from tutorial-modern.pdb" (molecule-name 41) 41 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 42) 42 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 43) 43 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb" (molecule-name 44) 44 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb3hfl.ent" 45 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz 2FOFCWT PH2FOFCWT" (molecule-name 46) 46 "Ideal-A-form-RNA" (molecule-name 47) 47 "Ideal-A-form-DNA" (molecule-name 48) 48 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 49) 49 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/some-waters-with-ter.pdb" (molecule-name 50) 50 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tm+some-waters.pdb" (molecule-name 51) 51 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/water-test-no-cell.pdb" (molecule-name 52) 52 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pathological-water-test.pdb" (molecule-name 53) 53 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 54 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" (molecule-name 55) 55 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 56) 56 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 57) 57 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 58) 58 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 59) 59 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2goz-manip.pdb" (molecule-name 60) 60 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/HOF.RES" (molecule-name 61) 61 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/hollander.ins" 64 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/insulin.fcf.cif Difference SigmaA" (molecule-name 65) 65 "atom selection from insulin.res" (molecule-name 66) 66 "atom selection from insulin.res" (molecule-name 68) 68 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/horma-p21.res" (molecule-name 69) 69 "new-horma.ins" (molecule-name 70) 70 "monomer-3GP.pdb" (molecule-name 71) 71 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb" (molecule-name 72) 72 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb" (molecule-name 73) 73 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb" (molecule-name 74) 74 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb" (molecule-name 75) 75 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb" (molecule-name 76) 76 "Copy of /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-NPO.pdb" (molecule-name 77) 77 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.pdb" 78 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz FWT PHWT" 79 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb43ca-sans-NPO-refmaced.mtz DELFWT PHDELWT" 80 "Masked (by protein)" (molecule-name 81) 81 "Fitted ligand #0" (molecule-name 82) 82 "Fitted ligand #1" (molecule-name 83) 83 "Fitted ligand #2" (molecule-name 84) 84 "Fitted ligand #3" (molecule-name 85) 85 "Fitted ligand #4" (molecule-name 86) 86 "Fitted ligand #5" (molecule-name 87) 87 "Fitted ligand #6" (molecule-name 88) 88 "Fitted ligand #7" (molecule-name 89) 89 "Fitted ligand #8" (molecule-name 90) 90 "Fitted ligand #9" (molecule-name 91) 91 "monomer-3GP.pdb" (molecule-name 92) 92 "Copy of monomer-3GP.pdb" (molecule-name 93) 93 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/dipole-residues.pdb" (molecule-name 94) 94 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" (molecule-name 95) 95 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/crashes_on_cootaneering.pdb" 96 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz FWT PHWT" (molecule-name 97) 97 "Ideal-A-form-RNA" (molecule-name 100) 100 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1wly.pdb" (molecule-name 101) 101 "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1yb5.pdb" do_Ca_plus_ligands_bonds with atom_colour_type 0 (graphics-to-ca-plus-ligands-representation 101) Entered testcase - SSM by atom selection [JED Example] (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2qd9.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2qd9.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2qd9.pdb has been read. Spacegroup: P 21 21 21 Cell: 65.65 74.36 78.98 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 102 read successfully (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2gtn.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2gtn.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/2gtn.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.986 74.554 78.029 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 0/337 Molecule 103 read successfully INFO:: reference 102 has 169 atoms selected INFO:: moving 103 has 169 atoms selected superposing... number of Ca atoms in selections: 21 (moving) and 21 (reference) Another Go... Moving Reference Distance A 140 <---> A 140 : 1.32979 A A 141 <---> A 141 : 1.26297 A A 142 <---> A 142 : 1.25076 A A 143 <---> A 143 : 1.22448 A A 144 <---> A 144 : 1.14246 A A 145 <---> A 145 : 1.15418 A A 146 <---> A 146 : 1.14197 A A 147 <---> A 147 : 1.14557 A A 148 <---> A 148 : 1.33121 A A 149 <---> A 149 : 1.19527 A A 150 <---> A 150 : 1.33849 A A 151 <---> A 151 : 1.1402 A A 152 <---> A 152 : 1.16023 A A 153 <---> A 153 : 1.25505 A A 154 <---> A 154 : 1.37155 A A 155 <---> A 155 : 1.57112 A A 156 <---> A 156 : 1.21499 A A 157 <---> A 157 : 1.16082 A A 158 <---> A 158 : 1.17177 A A 159 <---> A 159 : 1.10566 A A 160 <---> A 160 : 1.16949 A INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_2gtn.pdb_Thu_Sep_10_12:20:31_2009_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.9998, 0.009845, -0.01938| | -0.009814, 1, 0.001689| | 0.0194, -0.001498, 0.9998| ( 0.3207, 0.6598, 0.8819) Rotation - polar (omega,phi,kappa) 116.804 -94.6984 1.24908 Rotation - euler (alpha,beta,gamma) 175.02 1.11487 -175.583 Translation - Angstroms 0.320703 0.659802 0.881869 INFO: core rmsd achieved: 0.221041 Angstroems number of residues in reference structure: 330 number of residues in moving structure: 337 number of residues in aligned sections (reference): 21 number of residues in aligned sections (moving): 21 number of aligned residues: 21 number of gaps: 0 number of misdirections: 0 number of SSE combinations: 1 sequence identity: 100% Ended 06-ssm.scm Running 07-ncs.scm ... (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/insulin.res" 1) LATT LINE: LATT -2 SFAC LINE: SFAC C H N O S INFO:: CELL set to 77.726 77.726 77.726 90 90 90 INFO:: set space group to :I 21 3: READ-INS:: Spacegroup: I 21 3 INFO:: chain has 120 residues Symmetry available for this molecule Molecule 104 read successfully (read-shelx-ins-file "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/insulin.res") Entered testcase - NCS maps test (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.099 seconds to read MTZ file INFO:: 0.003 seconds to initialize map INFO:: 0.132 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.094 seconds for contour map INFO:: 0.338 seconds in total INFO:: NCS chain comparison 93/93 First atom of 720 in first selection 1/A/1/ASP/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 745 in second selection 1/B/1/ASP/ N altLoc :: segid :: pos: (13.876,16.167,23.033) B-factor: 20.03 INFO:: LSQ matched 93 atoms INFO:: 93 matched atoms had: mean devi: 1.17877 rms devi: 4.85919 max devi: 46.259 min devi: 0.125386 find_ncs_matrix returns (LSQ) | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2 maps contributing to the average INFO:: rescaling by 0.5 INFO:: 228096 out of 228096 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.000355334 st.d: 0.323619 Map statistics: min: -1.44957, max: 2.34115 -1.3548 4 -1.16527 12 -0.975731 37 -0.786195 453 -0.596659 4596 -0.407123 26403 -0.217587 59477 -0.0280514 58290 0.161484 36006 0.35102 20752 0.540556 11414 0.730092 5769 0.919628 2875 1.10916 1265 1.2987 484 1.48824 176 1.67777 54 1.86731 20 2.05684 7 2.24638 1 2.43592 1 INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.9637, -0.07462, -0.2563| | 0.2651, 0.3804, 0.886| | 0.0314, -0.9218, 0.3864| ( 38.09, -17.87, 14.32) inverse of reference matcher transformation: | 0.9637, 0.2651, 0.0314| | -0.07462, 0.3804, -0.9218| | -0.2563, 0.886, 0.3864| ( -32.42, 22.84, 20.06) boxing over uvw = ( -0.04469, -0.1739, -0.2816) to uvw = ( 1.228, 0.3332, 0.7985) INFO:: There were 2 maps contributing to the average INFO:: rescaling by 0.5 INFO:: 228096 out of 228096 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: 0.000355334 st.d: 0.323619 Map statistics: min: -1.44957, max: 2.34115 -1.3548 4 -1.16527 12 -0.975731 37 -0.786195 453 -0.596659 4596 -0.407123 26403 -0.217587 59477 -0.0280514 58290 0.161484 36006 0.35102 20752 0.540556 11414 0.730092 5769 0.919628 2875 1.10916 1265 1.2987 484 1.48824 176 1.67777 54 1.86731 20 2.05684 7 2.24638 1 2.43592 1 Entered testcase - NCS chains info NCS info: (("A" "B")) Entered testcase - NCS deviation info no diffs NCS target chain has 93 peers. resinfo: 93 92 to 93 92 diff: 0.82761 resinfo: 92 91 to 92 91 diff: 0.799087 resinfo: 91 90 to 91 90 diff: 1.30941 resinfo: 90 89 to 90 89 diff: 0.848865 resinfo: 89 88 to 89 88 diff: 3.47756 resinfo: 88 87 to 88 87 diff: 1.00522 resinfo: 87 86 to 87 86 diff: 0.793719 resinfo: 86 85 to 86 85 diff: 0.753689 resinfo: 85 84 to 85 84 diff: 0.809313 resinfo: 84 83 to 84 83 diff: 0.846976 resinfo: 83 82 to 83 82 diff: 0.88646 resinfo: 82 81 to 82 81 diff: 0.761955 resinfo: 81 80 to 81 80 diff: 0.804923 resinfo: 80 79 to 80 79 diff: 0.777717 resinfo: 79 78 to 79 78 diff: 0.606336 resinfo: 78 77 to 78 77 diff: 0.586572 resinfo: 77 76 to 77 76 diff: 0.605209 resinfo: 76 75 to 76 75 diff: 0.809205 resinfo: 75 74 to 75 74 diff: 0.473272 resinfo: 74 73 to 74 73 diff: 0.975401 resinfo: 73 72 to 73 72 diff: 0.597465 resinfo: 72 71 to 72 71 diff: 0.58493 resinfo: 71 70 to 71 70 diff: 0.606996 resinfo: 70 69 to 70 69 diff: 0.585566 resinfo: 69 68 to 69 68 diff: 0.64561 resinfo: 68 67 to 68 67 diff: 0.875328 resinfo: 67 66 to 67 66 diff: 0.864427 resinfo: 66 65 to 66 65 diff: 0.732479 resinfo: 65 64 to 65 64 diff: 0.401137 resinfo: 64 63 to 64 63 diff: 1.05664 resinfo: 63 62 to 63 62 diff: 2.85913 resinfo: 62 61 to 62 61 diff: 1.77684 resinfo: 61 60 to 61 60 diff: 1.97246 resinfo: 60 59 to 60 59 diff: 0.721019 resinfo: 59 58 to 59 58 diff: 0.873866 resinfo: 58 57 to 58 57 diff: 0.614926 resinfo: 57 56 to 57 56 diff: 0.604415 resinfo: 56 55 to 56 55 diff: 0.445784 resinfo: 55 54 to 55 54 diff: 0.356409 resinfo: 54 53 to 54 53 diff: 1.29157 resinfo: 53 52 to 53 52 diff: 0.456392 resinfo: 52 51 to 52 51 diff: 0.640025 resinfo: 51 50 to 51 50 diff: 0.545634 resinfo: 50 49 to 50 49 diff: 0.574687 resinfo: 49 48 to 49 48 diff: 0.512681 resinfo: 48 47 to 48 47 diff: 1.2413 resinfo: 47 46 to 47 46 diff: 0.96611 resinfo: 46 45 to 46 45 diff: 1.01008 resinfo: 45 44 to 45 44 diff: 0.968595 resinfo: 44 43 to 44 43 diff: 0.655634 resinfo: 43 42 to 43 42 diff: 0.705425 resinfo: 42 41 to 42 41 diff: 1.02306 resinfo: 41 40 to 41 40 diff: 1.80032 resinfo: 40 39 to 40 39 diff: 2.08207 resinfo: 39 38 to 39 38 diff: 0.401147 resinfo: 38 37 to 38 37 diff: 0.775939 resinfo: 37 36 to 37 36 diff: 0.613512 resinfo: 36 35 to 36 35 diff: 0.401273 resinfo: 35 34 to 35 34 diff: 0.26647 resinfo: 34 33 to 34 33 diff: 0.168051 resinfo: 33 32 to 33 32 diff: 0.246069 resinfo: 32 31 to 32 31 diff: 1.32047 resinfo: 31 30 to 31 30 diff: 1.15952 resinfo: 30 29 to 30 29 diff: 0.319934 resinfo: 29 28 to 29 28 diff: 0.527386 resinfo: 28 27 to 28 27 diff: 0.345661 resinfo: 27 26 to 27 26 diff: 0.55164 resinfo: 26 25 to 26 25 diff: 0.337172 resinfo: 25 24 to 25 24 diff: 0.745821 resinfo: 24 23 to 24 23 diff: 0.596737 resinfo: 23 22 to 23 22 diff: 0.492913 resinfo: 22 21 to 22 21 diff: 0.462489 resinfo: 21 20 to 21 20 diff: 0.507017 resinfo: 20 19 to 20 19 diff: 0.513467 resinfo: 19 18 to 19 18 diff: 0.435725 resinfo: 18 17 to 18 17 diff: 0.406794 resinfo: 17 16 to 17 16 diff: 0.391245 resinfo: 16 15 to 16 15 diff: 0.43917 resinfo: 15 14 to 15 14 diff: 0.503078 resinfo: 14 13 to 14 13 diff: 0.49505 resinfo: 13 12 to 13 12 diff: 0.580727 resinfo: 12 11 to 12 11 diff: 0.525931 resinfo: 11 10 to 11 10 diff: 0.559115 resinfo: 10 9 to 10 9 diff: 0.831857 resinfo: 9 8 to 9 8 diff: 0.94393 resinfo: 8 7 to 8 7 diff: 0.653129 resinfo: 7 6 to 7 6 diff: 0.863027 resinfo: 6 5 to 6 5 diff: 0.803605 resinfo: 5 4 to 5 4 diff: 0.753019 resinfo: 4 3 to 4 3 diff: 0.948347 resinfo: 3 2 to 3 2 diff: 1.08341 resinfo: 2 1 to 2 1 diff: 7.23927 resinfo: 1 0 to 1 0 diff: 0.894481 Entered testcase - NCS Residue Range copy (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 110 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:20:36_2009_modification_0.pdb.gz (delete-residue 110 "B" 1 "") INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:20:36_2009_modification_1.pdb.gz (delete-residue 110 "B" 2 "") INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:20:36_2009_modification_2.pdb.gz (delete-residue 110 "B" 3 "") %%%%%%%%% calling fill_ghost_info from c-interfac.cc make_ncs_ghosts_maybe INFO:: NCS chain comparison 90/93 First atom of 720 in first selection 1/A/1/ASP/ N altLoc :: segid :: pos: (44.878,12.955,8.761) B-factor: 30.17 First atom of 724 in second selection 1/B/4/GLY/ N altLoc :: segid :: pos: (18.183,22.264,18.93) B-factor: 21.71 INFO:: LSQ matched 90 atoms INFO:: 90 matched atoms had: mean devi: 0.364276 rms devi: 0.457135 max devi: 2.1351 min devi: 0.0880999 find_ncs_matrix returns (LSQ) | 0.9705, -0.04634, -0.2366| | 0.2357, 0.3884, 0.8908| | 0.05061, -0.9203, 0.3878| ( 37.8, -17.18, 13.82) INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:20:36_2009_modification_3.pdb.gz (setnum-from-serial-number 110 "B" 0) (setnum-from-serial-number 110 "B" 1) (setnum-from-serial-number 110 "B" 2) (setnum-from-serial-number 110 "B" 3) (setnum-from-serial-number 110 "B" 4) (setnum-from-serial-number 110 "B" 5) (setnum-from-serial-number 110 "B" 6) (setnum-from-serial-number 110 "B" 7) (setnum-from-serial-number 110 "B" 8) (setnum-from-serial-number 110 "B" 9) (setnum-from-serial-number 110 "B" 10) (setnum-from-serial-number 110 "B" 11) (setnum-from-serial-number 110 "B" 12) (setnum-from-serial-number 110 "B" 13) (setnum-from-serial-number 110 "B" 14) (setnum-from-serial-number 110 "B" 15) (setnum-from-serial-number 110 "B" 16) (setnum-from-serial-number 110 "B" 17) (setnum-from-serial-number 110 "B" 18) (setnum-from-serial-number 110 "B" 19) (setnum-from-serial-number 110 "B" 20) (setnum-from-serial-number 110 "B" 21) (setnum-from-serial-number 110 "B" 22) (setnum-from-serial-number 110 "B" 23) (setnum-from-serial-number 110 "B" 24) (setnum-from-serial-number 110 "B" 25) (setnum-from-serial-number 110 "B" 26) (setnum-from-serial-number 110 "B" 27) (setnum-from-serial-number 110 "B" 28) (setnum-from-serial-number 110 "B" 29) (setnum-from-serial-number 110 "B" 30) (setnum-from-serial-number 110 "B" 31) (setnum-from-serial-number 110 "B" 32) (setnum-from-serial-number 110 "B" 33) (setnum-from-serial-number 110 "B" 34) (setnum-from-serial-number 110 "B" 35) (setnum-from-serial-number 110 "B" 36) (setnum-from-serial-number 110 "B" 37) (setnum-from-serial-number 110 "B" 38) (setnum-from-serial-number 110 "B" 39) (setnum-from-serial-number 110 "B" 40) (setnum-from-serial-number 110 "B" 41) (setnum-from-serial-number 110 "B" 42) (setnum-from-serial-number 110 "B" 43) (setnum-from-serial-number 110 "B" 44) (setnum-from-serial-number 110 "B" 45) (setnum-from-serial-number 110 "B" 46) (setnum-from-serial-number 110 "B" 47) (setnum-from-serial-number 110 "B" 48) (setnum-from-serial-number 110 "B" 49) (setnum-from-serial-number 110 "B" 50) (setnum-from-serial-number 110 "B" 51) (setnum-from-serial-number 110 "B" 52) (setnum-from-serial-number 110 "B" 53) (setnum-from-serial-number 110 "B" 54) (setnum-from-serial-number 110 "B" 55) (setnum-from-serial-number 110 "B" 56) (setnum-from-serial-number 110 "B" 57) (setnum-from-serial-number 110 "B" 58) (setnum-from-serial-number 110 "B" 59) (setnum-from-serial-number 110 "B" 60) (setnum-from-serial-number 110 "B" 61) (setnum-from-serial-number 110 "B" 62) (setnum-from-serial-number 110 "B" 63) (setnum-from-serial-number 110 "B" 64) (setnum-from-serial-number 110 "B" 65) (setnum-from-serial-number 110 "B" 66) (setnum-from-serial-number 110 "B" 67) (setnum-from-serial-number 110 "B" 68) (setnum-from-serial-number 110 "B" 69) (setnum-from-serial-number 110 "B" 70) (setnum-from-serial-number 110 "B" 71) (setnum-from-serial-number 110 "B" 72) (setnum-from-serial-number 110 "B" 73) (setnum-from-serial-number 110 "B" 74) (setnum-from-serial-number 110 "B" 75) (setnum-from-serial-number 110 "B" 76) (setnum-from-serial-number 110 "B" 77) (setnum-from-serial-number 110 "B" 78) (setnum-from-serial-number 110 "B" 79) (setnum-from-serial-number 110 "B" 80) (setnum-from-serial-number 110 "B" 81) (setnum-from-serial-number 110 "B" 82) (setnum-from-serial-number 110 "B" 83) (setnum-from-serial-number 110 "B" 84) (setnum-from-serial-number 110 "B" 85) (setnum-from-serial-number 110 "B" 86) (setnum-from-serial-number 110 "B" 87) (setnum-from-serial-number 110 "B" 88) (setnum-from-serial-number 110 "B" 89) (setnum-from-serial-number 110 "B" 90) (setnum-from-serial-number 110 "B" 91) (setnum-from-serial-number 110 "B" 92) (setnum-from-serial-number 110 "B" 93) (setnum-from-serial-number 110 "B" 94) (setnum-from-serial-number 110 "B" 95) INFO:: mutate 2 A to a TRP INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:20:36_2009_modification_4.pdb.gz (mutate 2 "A" 110 "TRP") INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_12:20:36_2009_modification_5.pdb.gz Entered testcase - NCS Residue Range edit to all chains (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1t6q.ent" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1t6q.ent PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1t6q.ent has been read. Spacegroup: C 2 2 21 Cell: 60.041 112.491 111.298 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 110/110 INFO:: NCS chain comparison 110/110 INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Molecule 111 read successfully INFO:: mutate 50 A to a ASP INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb1t6q.ent_Thu_Sep_10_12:20:38_2009_modification_0.pdb.gz (mutate 50 "A" 111 "ASP") (is-solvent-chain-p 111 "C") %%%%%%%%% calling fill_ghost_info from c-interfac.cc make_ncs_ghosts_maybe INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7/GLY/ N altLoc :: segid :: pos: (31.795,49.973,50.866) B-factor: 68.18 First atom of 893 in second selection 1/B/6/CYS/ N altLoc :: segid :: pos: (45.362,34.24,30.671) B-factor: 84.36 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.20482 rms devi: 0.265098 max devi: 1.17072 min devi: 0.0159991 find_ncs_matrix returns (LSQ) | 0.5407, 0.4775, 0.6926| | -0.4862, -0.4944, 0.7205| | 0.6865, -0.7263, -0.03511| ( -28.15, 65.89, 42.9) INFO:: NCS chain comparison 109/110 First atom of 881 in first selection 1/A/7/GLY/ N altLoc :: segid :: pos: (31.795,49.973,50.866) B-factor: 68.18 First atom of 881 in second selection 1/C/7/GLY/ N altLoc :: segid :: pos: (47.664,58.992,25.996) B-factor: 67.72 INFO:: LSQ matched 110 atoms INFO:: 110 matched atoms had: mean devi: 0.227456 rms devi: 0.303489 max devi: 1.65495 min devi: 0.0660944 find_ncs_matrix returns (LSQ) | 0.5303, -0.4851, 0.6953| | 0.4758, -0.5085, -0.7177| | 0.7017, 0.7114, -0.03884| ( 18.19, 77.78, -25.69) INFO:: fill_ghost_info Constructed 2 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb1t6q.ent_Thu_Sep_10_12:20:38_2009_modification_1.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb1t6q.ent_Thu_Sep_10_12:20:38_2009_modification_2.pdb.gz result: (#t #t) Entered testcase - Manual NCS ghosts generates correct NCS chain ids (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1hvv.ent" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1hvv.ent PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 Cell: 88.32 88.32 115.62 90 90 120 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 112 read successfully DEBUG ncs_control_change_ncs_master_to_chain_id imol: 112 and chain_id: B %%%%%% add_ncs_ghosts_using_ncs_master %%%%%% imaster: 1 Checking chains for NCS matching to chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193/SER/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 First atom of 540 in second selection 1/A/190/GLN/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.49888 rms devi: 2.79624 max devi: 6.68599 min devi: 0.440067 find_ncs_matrix returns (LSQ) | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) Adding ghost with name: NCS found from matching Chain A onto Chain B INFO:: NCS chain comparison 62/62 First atom of 506 in first selection 1/B/193/SER/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 First atom of 535 in second selection 1/C/190/GLN/ N altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.76 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.6728 rms devi: 2.9369 max devi: 6.12 min devi: 0.248273 find_ncs_matrix returns (LSQ) | -0.3504, -0.8022, -0.4834| | -0.7587, -0.05952, 0.6488| | -0.5492, 0.594, -0.5878| ( -29.05, 14.61, -72.53) Adding ghost with name: NCS found from matching Chain C onto Chain B INFO:: NCS chain comparison 61/62 First atom of 506 in first selection 1/B/193/SER/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 First atom of 497 in second selection 1/D/193/SER/ N altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.35 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 1.73174 rms devi: 1.9769 max devi: 7.94534 min devi: 0.52974 find_ncs_matrix returns (LSQ) | -0.3815, -0.9208, -0.08098| | -0.9191, 0.3685, 0.1396| | -0.09874, 0.1277, -0.9869| ( -11.18, 4.757, -127.2) Adding ghost with name: NCS found from matching Chain D onto Chain B INFO:: NCS chain comparison 0/62 INFO:: set_ncs_master_chain Constructed 3 ghosts Ghost info:: NCS found from matching Chain A onto Chain B Ghost info:: NCS found from matching Chain C onto Chain B Ghost info:: NCS found from matching Chain D onto Chain B Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 112) INFO:: Matching/moving molecule number 113 to 112 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.223919 rms devi: 0.23495 max devi: 0.3369 min devi: 0.0588188 INFO:: Axis orientation: ( 0.7368, 0.6481, 0.1925) INFO:: Rotation in CCP4 Polar Angles: Polar = (78.9031,41.336,116.426) INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb1hvv.ent_Thu_Sep_10_12:20:42_2009_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | 0.3395, 0.5177, 0.7853| | 0.8624, 0.162, -0.4796| | -0.3755, 0.8401, -0.3915| ( 90.55, -91.12, -47.52) INFO:: fractional coordinates matrix: | 0.8374, 0.1106, 0.6656| | 0.9958, -0.3359, -0.7249| | -0.2868, 0.6992, -0.3915| ( 0.4296, -1.191, -0.411) (close-molecule 113) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 112) INFO:: Matching/moving molecule number 114 to 112 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.194298 rms devi: 0.211186 max devi: 0.358313 min devi: 0.0328719 INFO:: Axis orientation: ( -0.431, 0.3986, 0.8095) INFO:: Rotation in CCP4 Polar Angles: Polar = (144.051,-42.7613,171.905) INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb1hvv.ent_Thu_Sep_10_12:20:42_2009_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.6203, -0.2279, -0.7505| | -0.4559, -0.6739, 0.5814| | -0.6382, 0.7028, 0.3141| ( -22.14, -19.93, 1.626) INFO:: fractional coordinates matrix: | -0.8835, -0.09252, -0.543| | -0.5264, -0.4107, 0.8789| | -0.4875, 0.7087, 0.3141| ( -0.381, -0.2605, 0.01406) (close-molecule 114) Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 112) INFO:: Matching/moving molecule number 115 to 112 INFO:: LSQ matched 44 atoms INFO:: 44 matched atoms had: mean devi: 0.417399 rms devi: 0.453088 max devi: 0.792632 min devi: 0.0759332 INFO:: Axis orientation: ( 0.6231, -0.7786, -0.07411) INFO:: Rotation in CCP4 Polar Angles: Polar = (85.7498,128.67,177.232) INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb1hvv.ent_Thu_Sep_10_12:20:42_2009_modification_0.pdb.gz INFO:: coordinates transformed by orthonal matrix: | -0.2227, -0.9733, -0.05471| | -0.9662, 0.2129, 0.1454| | -0.1299, 0.08525, -0.9879| ( -15.82, -0.3228, -130) INFO:: fractional coordinates matrix: | -0.7806, -0.3462, 0.03831| | -1.116, 0.7707, 0.2198| | -0.09924, 0.106, -0.9879| ( -0.1813, -0.00422, -1.125) (close-molecule 115) NCS ghost chain IDs pre: (("B" "A" "C" "D")) NCS ghost chain IDs post: (("B" "A" "C" "D")) Entered testcase - NCS maps overwrite existing maps (molecule-name 0) (molecule-name 1) (molecule-name 6) (molecule-name 7) (molecule-name 8) (molecule-name 10) (molecule-name 11) (molecule-name 12) (molecule-name 13) (molecule-name 14) (molecule-name 16) (molecule-name 17) (molecule-name 18) (molecule-name 19) (molecule-name 20) (molecule-name 22) (molecule-name 23) (molecule-name 26) (molecule-name 33) (molecule-name 34) (molecule-name 35) (molecule-name 36) (molecule-name 37) (molecule-name 38) (molecule-name 39) (molecule-name 40) (molecule-name 41) (molecule-name 42) (molecule-name 43) (molecule-name 44) (molecule-name 46) (molecule-name 47) (molecule-name 48) (molecule-name 49) (molecule-name 50) (molecule-name 51) (molecule-name 52) (molecule-name 53) (molecule-name 55) (molecule-name 56) (molecule-name 57) (molecule-name 58) (molecule-name 59) (molecule-name 60) (molecule-name 61) (molecule-name 65) (molecule-name 66) (molecule-name 68) (molecule-name 69) (molecule-name 70) (molecule-name 71) (molecule-name 72) (molecule-name 73) (molecule-name 74) (molecule-name 75) (molecule-name 76) (molecule-name 77) (molecule-name 81) (molecule-name 82) (molecule-name 83) (molecule-name 84) (molecule-name 85) (molecule-name 86) (molecule-name 87) (molecule-name 88) (molecule-name 89) (molecule-name 90) (molecule-name 91) (molecule-name 92) (molecule-name 93) (molecule-name 94) (molecule-name 95) (molecule-name 97) (molecule-name 100) (molecule-name 101) (molecule-name 102) (molecule-name 103) (molecule-name 104) (close-molecule 106) (close-molecule 108) (molecule-name 110) (molecule-name 111) (molecule-name 112) (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1hvv.ent" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1hvv.ent PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb1hvv.ent has been read. Spacegroup: P 31 2 1 Cell: 88.32 88.32 115.62 90 90 120 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 62/67 INFO:: NCS chain comparison 66/67 INFO:: NCS chain comparison 61/67 INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" Molecule 116 read successfully (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1hvv_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/1hvv_sigmaa.mtz Number of OBSERVED reflections: 20903 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 112, 112, 150) INFO:: 0.191 seconds to read MTZ file INFO:: 0.176 seconds to initialize map INFO:: 0.229 seconds for FFT INFO:: 0.044 seconds for statistics Map mean: ........ -1.58386e-06 Map sigma: ....... 0.224074 Map maximum: ..... 1.72187 Map minimum: ..... -0.88179 INFO:: 0.049 seconds for contour map INFO:: 0.689 seconds in total INFO:: NCS chain comparison 62/67 First atom of 540 in first selection 1/A/190/GLN/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 First atom of 506 in second selection 1/B/193/SER/ N altLoc :: segid :: pos: (0.57,-74.72,-82.848) B-factor: 88.52 INFO:: LSQ matched 62 atoms INFO:: 62 matched atoms had: mean devi: 2.49888 rms devi: 2.79624 max devi: 6.68599 min devi: 0.440067 find_ncs_matrix returns (LSQ) | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) INFO:: NCS chain comparison 66/67 First atom of 540 in first selection 1/A/190/GLN/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 First atom of 535 in second selection 1/C/190/GLN/ N altLoc :: segid :: pos: (63.726,-15.709,-72.885) B-factor: 50.76 INFO:: LSQ matched 66 atoms INFO:: 66 matched atoms had: mean devi: 1.97132 rms devi: 2.1729 max devi: 4.54109 min devi: 0.429522 find_ncs_matrix returns (LSQ) | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) INFO:: NCS chain comparison 61/67 First atom of 540 in first selection 1/A/190/GLN/ N altLoc :: segid :: pos: (-13.535,-64.438,-56.928) B-factor: 45.26 First atom of 497 in second selection 1/D/193/SER/ N altLoc :: segid :: pos: (62.917,-35.989,-55.929) B-factor: 78.35 INFO:: LSQ matched 61 atoms INFO:: 61 matched atoms had: mean devi: 3.70416 rms devi: 4.0859 max devi: 9.43828 min devi: 0.285802 find_ncs_matrix returns (LSQ) | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) INFO:: NCS chain comparison 0/67 INFO:: fill_ghost_info Constructed 3 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Ghost 1 name: "NCS found from matching Chain C onto Chain A" Ghost 2 name: "NCS found from matching Chain D onto Chain A" INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4 maps contributing to the average INFO:: rescaling by 0.25 INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.000831257 st.d: 0.176659 Map statistics: min: -0.997714, max: 1.48656 -0.935607 4 -0.811393 18 -0.687179 139 -0.562965 686 -0.438751 3580 -0.314537 13684 -0.190323 43824 -0.0661091 105065 0.0581049 85978 0.182319 35332 0.306533 15215 0.430747 6067 0.554961 2422 0.679175 947 0.803388 405 0.927602 206 1.05182 85 1.17603 38 1.30024 9 1.42446 8 1.54867 0 INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4 maps contributing to the average INFO:: rescaling by 0.25 INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.000831257 st.d: 0.176659 Map statistics: min: -0.997714, max: 1.48656 -0.935607 4 -0.811393 18 -0.687179 139 -0.562965 686 -0.438751 3580 -0.314537 13684 -0.190323 43824 -0.0661091 105065 0.0581049 85978 0.182319 35332 0.306533 15215 0.430747 6067 0.554961 2422 0.679175 947 0.803388 405 0.927602 206 1.05182 85 1.17603 38 1.30024 9 1.42446 8 1.54867 0 INFO:: installing ghost map with name :NCS found from matching Chain B onto Chain A Done install_ghost_map INFO:: installing ghost map with name :NCS found from matching Chain C onto Chain A Done install_ghost_map INFO:: installing ghost map with name :NCS found from matching Chain D onto Chain A Done install_ghost_map Reference matcher: 0 and 0 | 0.7026, 0.6024, -0.3788| | 0.1278, 0.4169, 0.8999| | 0.7, -0.6807, 0.2159| ( 5.528, 36.75, -101.2) inverse of reference matcher transformation: | 0.7026, 0.1278, 0.7| | 0.6024, 0.4169, -0.6807| | -0.3788, 0.8999, 0.2159| ( 62.25, -87.53, -9.128) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 1 | -0.4445, -0.8903, -0.09887| | -0.893, 0.4317, 0.1271| | -0.07049, 0.1448, -0.9869| ( -8.624, 7.402, -127.7) inverse of reference matcher transformation: | -0.4445, -0.893, -0.07049| | -0.8903, 0.4317, 0.1448| | -0.09887, 0.1271, -0.9869| ( -6.223, 7.613, -127.8) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) Reference matcher: 0 and 2 | -0.7198, -0.6079, 0.3353| | -0.5986, 0.2989, -0.7432| | 0.3516, -0.7356, -0.579| ( 36.14, -61.4, -149.3) inverse of reference matcher transformation: | -0.7198, -0.5986, 0.3516| | -0.6079, 0.2989, -0.7356| | 0.3353, -0.7432, -0.579| ( 41.75, -69.53, -144.2) boxing over uvw = ( -0.7364, -0.9448, -0.679) to uvw = ( 0.7947, 0.04686, -0.4302) INFO:: There were 4 maps contributing to the average INFO:: rescaling by 0.25 INFO:: 313712 out of 313712 (100%) map points were masked out of NCS average target volume, chain A INFO:: made 1 averaged map(s) Map statistics: mean: -0.000831257 st.d: 0.176659 Map statistics: min: -0.997714, max: 1.48656 -0.935607 4 -0.811393 18 -0.687179 139 -0.562965 686 -0.438751 3580 -0.314537 13684 -0.190323 43824 -0.0661091 105065 0.0581049 85978 0.182319 35332 0.306533 15215 0.430747 6067 0.554961 2422 0.679175 947 0.803388 405 0.927602 206 1.05182 85 1.17603 38 1.30024 9 1.42446 8 1.54867 0 (molecule-name 0) (molecule-name 1) (molecule-name 6) (molecule-name 7) (molecule-name 8) (molecule-name 10) (molecule-name 11) (molecule-name 12) (molecule-name 13) (molecule-name 14) (molecule-name 16) (molecule-name 17) (molecule-name 18) (molecule-name 19) (molecule-name 20) (molecule-name 22) (molecule-name 23) (molecule-name 26) (molecule-name 33) (molecule-name 34) (molecule-name 35) (molecule-name 36) (molecule-name 37) (molecule-name 38) (molecule-name 39) (molecule-name 40) (molecule-name 41) (molecule-name 42) (molecule-name 43) (molecule-name 44) (molecule-name 46) (molecule-name 47) (molecule-name 48) (molecule-name 49) (molecule-name 50) (molecule-name 51) (molecule-name 52) (molecule-name 53) (molecule-name 55) (molecule-name 56) (molecule-name 57) (molecule-name 58) (molecule-name 59) (molecule-name 60) (molecule-name 61) (molecule-name 65) (molecule-name 66) (molecule-name 68) (molecule-name 69) (molecule-name 70) (molecule-name 71) (molecule-name 72) (molecule-name 73) (molecule-name 74) (molecule-name 75) (molecule-name 76) (molecule-name 77) (molecule-name 81) (molecule-name 82) (molecule-name 83) (molecule-name 84) (molecule-name 85) (molecule-name 86) (molecule-name 87) (molecule-name 88) (molecule-name 89) (molecule-name 90) (molecule-name 91) (molecule-name 92) (molecule-name 93) (molecule-name 94) (molecule-name 95) (molecule-name 97) (molecule-name 100) (molecule-name 101) (molecule-name 102) (molecule-name 103) (molecule-name 104) (molecule-name 110) (molecule-name 111) (molecule-name 112) (molecule-name 116) ==== "NCS found from matching Chain B onto Chain A" 2 (molecule-name 0) (molecule-name 1) (molecule-name 6) (molecule-name 7) (molecule-name 8) (molecule-name 10) (molecule-name 11) (molecule-name 12) (molecule-name 13) (molecule-name 14) (molecule-name 16) (molecule-name 17) (molecule-name 18) (molecule-name 19) (molecule-name 20) (molecule-name 22) (molecule-name 23) (molecule-name 26) (molecule-name 33) (molecule-name 34) (molecule-name 35) (molecule-name 36) (molecule-name 37) (molecule-name 38) (molecule-name 39) (molecule-name 40) (molecule-name 41) (molecule-name 42) (molecule-name 43) (molecule-name 44) (molecule-name 46) (molecule-name 47) (molecule-name 48) (molecule-name 49) (molecule-name 50) (molecule-name 51) (molecule-name 52) (molecule-name 53) (molecule-name 55) (molecule-name 56) (molecule-name 57) (molecule-name 58) (molecule-name 59) (molecule-name 60) (molecule-name 61) (molecule-name 65) (molecule-name 66) (molecule-name 68) (molecule-name 69) (molecule-name 70) (molecule-name 71) (molecule-name 72) (molecule-name 73) (molecule-name 74) (molecule-name 75) (molecule-name 76) (molecule-name 77) (molecule-name 81) (molecule-name 82) (molecule-name 83) (molecule-name 84) (molecule-name 85) (molecule-name 86) (molecule-name 87) (molecule-name 88) (molecule-name 89) (molecule-name 90) (molecule-name 91) (molecule-name 92) (molecule-name 93) (molecule-name 94) (molecule-name 95) (molecule-name 97) (molecule-name 100) (molecule-name 101) (molecule-name 102) (molecule-name 103) (molecule-name 104) (molecule-name 110) (molecule-name 111) (molecule-name 112) (molecule-name 116) ==== "NCS found from matching Chain C onto Chain A" 2 (molecule-name 0) (molecule-name 1) (molecule-name 6) (molecule-name 7) (molecule-name 8) (molecule-name 10) (molecule-name 11) (molecule-name 12) (molecule-name 13) (molecule-name 14) (molecule-name 16) (molecule-name 17) (molecule-name 18) (molecule-name 19) (molecule-name 20) (molecule-name 22) (molecule-name 23) (molecule-name 26) (molecule-name 33) (molecule-name 34) (molecule-name 35) (molecule-name 36) (molecule-name 37) (molecule-name 38) (molecule-name 39) (molecule-name 40) (molecule-name 41) (molecule-name 42) (molecule-name 43) (molecule-name 44) (molecule-name 46) (molecule-name 47) (molecule-name 48) (molecule-name 49) (molecule-name 50) (molecule-name 51) (molecule-name 52) (molecule-name 53) (molecule-name 55) (molecule-name 56) (molecule-name 57) (molecule-name 58) (molecule-name 59) (molecule-name 60) (molecule-name 61) (molecule-name 65) (molecule-name 66) (molecule-name 68) (molecule-name 69) (molecule-name 70) (molecule-name 71) (molecule-name 72) (molecule-name 73) (molecule-name 74) (molecule-name 75) (molecule-name 76) (molecule-name 77) (molecule-name 81) (molecule-name 82) (molecule-name 83) (molecule-name 84) (molecule-name 85) (molecule-name 86) (molecule-name 87) (molecule-name 88) (molecule-name 89) (molecule-name 90) (molecule-name 91) (molecule-name 92) (molecule-name 93) (molecule-name 94) (molecule-name 95) (molecule-name 97) (molecule-name 100) (molecule-name 101) (molecule-name 102) (molecule-name 103) (molecule-name 104) (molecule-name 110) (molecule-name 111) (molecule-name 112) (molecule-name 116) ==== "NCS found from matching Chain D onto Chain A" 2 Ended 07-ncs.scm Running 08-utils.scm ... Entered testcase - Test key symbols Entered testcase - Test running a Python function DEBUG:: in safe_python_command_with_return() pValue is 0x95d6904 DEBUG:: in safe_python_command_with_return() pValue is 0 error (syntax error) DEBUG:: in safe_python_command_with_return() pValue is 0x95d6934 DEBUG:: in safe_python_command_with_return() pValue is 0 error (syntax error) DEBUG:: in safe_python_command_with_return() pValue is 0x978a324 WARNING:: py_clean_internal: incomprehensible argument passed (1, 2, 3) test_val_2 passed DEBUG:: in safe_python_command_with_return() pValue is 0 error (not syntax error) Traceback (most recent call last): File "", line 1, in NameError: name 'rr_not_found_thing' is not defined test_val_3 passed Entered testcase - Internal/External Molecule Numbers match Ended 08-utils.scm === greg-tests Summary === # of testcases attempted 92 # of expected passes 90 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 2 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 === Summary of all tests === # of tools 1 # of testcases attempted 92 # of expected passes 90 # of expected failures 0 # of unexpected passes 0 # of unexpected failures 2 # of unresolved testcases 0 # of unsupported testcases 0 # of untested testcases 0 # of files abandoned 0 (stereo-mode-state) State file 0-coot.state.scm written. (save-state) State file 0-coot-history.py written. State file 0-coot-history.scm written. Some deprecated features have been used. Set the environment variable GUILE_WARN_DEPRECATED to "detailed" and rerun the program to get more information. Set it to "no" to suppress this message. * * ERROR: sci-chemistry/coot-9999 failed. * Call stack: * ebuild.sh, line 49: Called src_test * environment, line 3347: Called die * The specific snippet of code: * ${S}/src/coot-real --no-graphics --script command-line-greg.scm || die; * The die message: * (no error message) * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-chemistry/coot-9999/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/coot-9999/temp/environment'. * This ebuild is from an overlay named 'science': '/home/data/local/science/' * >>> Checking greg-data.tar.gz's mtime... >>> WORKDIR is up-to-date, keeping... >>> It appears that 'coot-9999' is already prepared; skipping. >>> Remove '/var/tmp/portage/sci-chemistry/coot-9999/.prepared' to force prepare. >>> It appears that 'coot-9999' is already configured; skipping. >>> Remove '/var/tmp/portage/sci-chemistry/coot-9999/.configured' to force configuration. >>> It appears that 'coot-9999' is already compiled; skipping. >>> Remove '/var/tmp/portage/sci-chemistry/coot-9999/.compiled' to force compilation. INFO:: splash_screen_pixmap_dir /var/tmp/portage/sci-chemistry/coot-9999/work/pixmaps INFO:: Colours file: /var/tmp/portage/sci-chemistry/coot-9999/work/colours.def loaded There are 118 data in /usr/share/ccp4//data/monomers/list/mon_lib_list.cif There are 2 data in /usr/share/ccp4//data/monomers/a/ALA.cif There are 2 data in /usr/share/ccp4//data/monomers/a/ASP.cif There are 2 data in /usr/share/ccp4//data/monomers/a/ASN.cif There are 2 data in /usr/share/ccp4//data/monomers/c/CYS.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GLN.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GLY.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GLU.cif There are 2 data in /usr/share/ccp4//data/monomers/p/PHE.cif There are 2 data in /usr/share/ccp4//data/monomers/h/HIS.cif There are 2 data in /usr/share/ccp4//data/monomers/i/ILE.cif There are 2 data in /usr/share/ccp4//data/monomers/l/LYS.cif There are 2 data in /usr/share/ccp4//data/monomers/l/LEU.cif There are 2 data in /usr/share/ccp4//data/monomers/m/MET.cif There are 2 data in /usr/share/ccp4//data/monomers/m/MSE.cif There are 2 data in /usr/share/ccp4//data/monomers/p/PRO.cif There are 2 data in /usr/share/ccp4//data/monomers/a/ARG.cif There are 2 data in /usr/share/ccp4//data/monomers/s/SER.cif There are 2 data in /usr/share/ccp4//data/monomers/t/THR.cif There are 2 data in /usr/share/ccp4//data/monomers/v/VAL.cif There are 2 data in /usr/share/ccp4//data/monomers/t/TRP.cif There are 2 data in /usr/share/ccp4//data/monomers/t/TYR.cif There are 2 data in /usr/share/ccp4//data/monomers/p/PO4.cif There are 2 data in /usr/share/ccp4//data/monomers/s/SO4.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GOL.cif There are 2 data in /usr/share/ccp4//data/monomers/e/ETH.cif There are 2 data in /usr/share/ccp4//data/monomers/c/CIT.cif There are 2 data in /usr/share/ccp4//data/monomers/a/AR.cif There are 2 data in /usr/share/ccp4//data/monomers/a/AD.cif There are 2 data in /usr/share/ccp4//data/monomers/c/CR.cif There are 2 data in /usr/share/ccp4//data/monomers/c/CD.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GR.cif There are 2 data in /usr/share/ccp4//data/monomers/g/GD.cif There are 2 data in /usr/share/ccp4//data/monomers/t/TD.cif There are 2 data in /usr/share/ccp4//data/monomers/u/UR.cif Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/standard-residues.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) DEBUG:: stating pydirectory /var/tmp/portage/sci-chemistry/coot-9999/work/python INFO:: importing coot.py from /var/tmp/portage/sci-chemistry/coot-9999/work/python/coot.py Importing python module coot using command from coot import * INFO:: coot.py imported INFO loading coot python modules Running python script /var/tmp/portage/sci-chemistry/coot-9999/work/python/coot_load_modules.py Loading: coot_utils.py Loading: filter.py Loading: coot_lsq.py Loading: shelx.py Loading: get_ebi.py Loading: local_code.py Loading: hello.py Good Afternoon Justin, Welcome to Coot. (set-display-intro-string "Good Afternoon Justin, Welcome to Coot.") Loading: mutate.py Loading: refmac.py Loading: libcheck.py Loading: gap.py Loading: fitting.py Loading: raster3d.py Loading: povray.py Loading: remote_control.py Loading: generic_objects.py Loading: ncs.py Loading: cns2coot.py Loading: tips.py Loading: americanisms.py Loading: group_settings.py Loading: brute_lsqman.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /var/tmp/portage/sci-chemistry/coot-9999/work/scheme/ load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" WARNING: (net http client): imported module (net http message) overrides core binding `version' load "local-code.scm" load "hello.scm" Good afternoon . Welcome to Coot. (set-display-intro-string "Good afternoon . Welcome to Coot") load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "parse-pisa-xml.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "americanisms.scm" load "group-settings.scm" (set-display-lists-for-maps 0) (filter-fileselection-filenames-state) (get-active-map-drag-flag) === greg-tests tests === Loading greg-tests/begin.grg ... =============================================================== ==================== Testing ================================== =============================================================== Loaded greg-tests/begin.grg Running 01-pdb+mtz.scm ... Entered testcase - Post Go To Atom no molecules (post-go-to-atom-window) Entered testcase - Close bad molecule (close-molecule -2) Entered testcase - Read coordinates test (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully Entered testcase - New molecule from bogus molecule Molecule number -5 is not a valid model molecule Entered testcase - New molecule from bogus atom selection in new_molecule_by_atom_selection Something bad happened - No atoms selected (info-dialog "Oops, failed to create fragment. No atoms selected Incorrect atom specifier? "//A/100"") INFO:: pre-n-molecules 1 post-n-molecules 1 Entered testcase - ins code change and Goto atom over an ins code break (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/ins-code-fragment-pre.pdb" 0) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/ins-code-fragment-pre.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 1 read successfully (set-go-to-atom-molecule 1) DEBUG:: Found chain_id A (change-residue-number 1 "A" 68 "" 68 "A") DEBUG:: Found chain_id A (change-residue-number 1 "A" 69 "" 68 "B") DEBUG:: Found chain_id A (change-residue-number 1 "A" 67 "" 68 "") pre and post ins codes: "" "A" pass: ("A" 68 "" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 70 "" " CA ") pass: ("A" 62 "" " CA ") pass: ("A" 68 "B" " CA ") pass: ("A" 68 "A" " CA ") pass: ("A" 68 "" " CA ") pass: ("A" 66 "" " CA ") Entered testcase - Read a bogus map WARNING:: Error reading bogus.map Read map bogus.map failed Entered testcase - Read MTZ test WARNING:: Can't find file bogus.mtz (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.389 seconds to read MTZ file INFO:: 0.149 seconds to initialize map INFO:: 0.282 seconds for FFT INFO:: 0.01 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.163 seconds for contour map INFO:: 0.993 seconds in total Entered testcase - Map Sigma INFO:: map sigmas 0.311501026153564 #f Entered testcase - Another Level Test making conventional map from MTZ filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.076 seconds to read MTZ file INFO:: 0.003 seconds to initialize map INFO:: 0.104 seconds for FFT INFO:: 0.009 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.033 seconds for contour map INFO:: 0.225 seconds in total (make-and-draw-map-with-reso-with-refmac-params "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0 0 "Fobs:None-specified" "SigF:None-specified" "RFree:None-specified" 0 0 0 0.00 0.00) (another-level-from-map-molecule-number 2) Entered testcase - Sharpen map from map (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.104 seconds to read MTZ file INFO:: 0.036 seconds to initialize map INFO:: 0.065 seconds for FFT INFO:: 0.008 seconds for statistics Map mean: ........ 3.31773e-12 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.007 seconds for contour map INFO:: 0.22 seconds in total INFO:: map file type was determined to be CCP4 type allocating space in read_ccp4_map attempting to read CCP4 map: test-3hfl.map closing CCP4 map: test-3hfl.map Map statistics: mean: 3.31773e-12 st.d: 0.260405 Map statistics: min: -1.03389, max: 1.71787 -0.965098 9 -0.82751 119 -0.689922 1019 -0.552334 4514 -0.414746 13139 -0.277158 28550 -0.13957 59504 -0.00198239 84317 0.135606 44993 0.273194 14815 0.410781 9178 0.548369 7021 0.685957 4753 0.823545 2717 0.961133 1265 1.09872 403 1.23631 108 1.3739 34 1.51149 18 1.64907 3 1.78666 1 Map mean: ........ 3.31773e-12 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 Entered testcase - Set Atom Attribute Test (set-atom-attribute 0 "A" 11 "" " CA " "" "x" 64.5) Entered testcase - Add Terminal Residue Test (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 6 read successfully INFO:: Masking around 41 atoms fitting terminal residue with rigid body refinement using 100 trials INFO:: Fitting terminal residue with individual rigid body fitting. INFO:: found better residue, score: 3.50214 INFO:: found better residue, score: 3.9272 INFO:: found better residue, score: 4.379 INFO:: found better residue, score: 4.61148 A 0 ALA N :: xyz = ( 49.2, 12.74, 4.454) A 0 ALA C :: xyz = ( 50.2, 13.69, 2.416) A 0 ALA CA :: xyz = ( 49.88, 13.9, 3.891) A 0 ALA O :: xyz = ( 51.28, 14.01, 1.91) !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: mutating residue in add_cb_to_terminal_res INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Sep_10_13:00:05_2009_modification_0.pdb.gz (add-terminal-residue 6 "A" 1 1) (write-pdb-file 6 "regression-test-terminal-residue.pdb") In new_molecule_by_atom_selection has contains chain id A Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) INFO:: backup file coot-backup/atom_selection_from_tutorial-add-terminal-1-test.pdb_Thu_Sep_10_13:00:05_2009_modification_0.pdb.gz (rotation-centre-position 0) (rotation-centre-position 1) (rotation-centre-position 2) Entered testcase - Select by Sphere Symmetry available for this molecule (n-chains 8) (chain_id 8 0) Sphere mol: there are 4 residues in chain "B" (resname-from-serial-number 8 "B" 0) (setnum-from-serial-number 8 "B" 0) (insertion-code-from-serial-number 8 "B" 0) (resname-from-serial-number 8 "B" 1) (setnum-from-serial-number 8 "B" 1) (insertion-code-from-serial-number 8 "B" 1) (resname-from-serial-number 8 "B" 2) (setnum-from-serial-number 8 "B" 2) (insertion-code-from-serial-number 8 "B" 2) (resname-from-serial-number 8 "B" 3) (setnum-from-serial-number 8 "B" 3) (insertion-code-from-serial-number 8 "B" 3) Found 20 sphere atoms Entered testcase - Test Views (go-to-view-number 0 1) Entered testcase - Label Atoms and Delete In new_molecule_by_atom_selection has contains chain id B Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (set-rotation-centre 31.464 21.413 14.824) N /10/B is not found in this molecule: (9) atom selection from tutorial-modern.pdb INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_13:00:05_2009_modification_0.pdb.gz (delete-residue 9 "B" 10 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_13:00:05_2009_modification_1.pdb.gz (delete-residue 9 "B" 11 "") INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_13:00:05_2009_modification_2.pdb.gz (delete-residue 9 "B" 12 "") Entered testcase - Rotamer outliers (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rotamer-test-fragment.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rotamer-test-fragment.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rotamer-test-fragment.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 10 read successfully INFO:: Reading rotamer probability tables...Failed to read rotamer probability table for SER Failed to open /usr/share/coot/rama-data/rota500-ser.data Failed to read rotamer probability table for VAL Failed to open /usr/share/coot/rama-data/rota500-val.data Failed to read rotamer probability table for THR Failed to open /usr/share/coot/rama-data/rota500-thr.data Failed to read rotamer probability table for CYS Failed to open /usr/share/coot/rama-data/rota500-cys.data Failed to read rotamer probability table for PRO Failed to open /usr/share/coot/rama-data/rota500-pro.data Failed to read rotamer probability table for ASN Failed to open /usr/share/coot/rama-data/rota500-asn.data Failed to read rotamer probability table for ASP Failed to open /usr/share/coot/rama-data/rota500-asp.data Failed to read rotamer probability table for PHE Failed to open /usr/share/coot/rama-data/rota500-phetyr.data Failed to read rotamer probability table for TYR Failed to open /usr/share/coot/rama-data/rota500-phetyr.data Failed to read rotamer probability table for TRP Failed to open /usr/share/coot/rama-data/rota500-trp.data Failed to read rotamer probability table for HIS Failed to open /usr/share/coot/rama-data/rota500-his.data Failed to read rotamer probability table for ILE Failed to open /usr/share/coot/rama-data/rota500-ile.data Failed to read rotamer probability table for LEU Failed to open /usr/share/coot/rama-data/rota500-leu.data Failed to read rotamer probability table for MET Failed to open /usr/share/coot/rama-data/rota500-met.data Failed to read rotamer probability table for MSE Failed to open /usr/share/coot/rama-data/rota500-met.data Failed to read rotamer probability table for GLU Failed to open /usr/share/coot/rama-data/rota500-glu.data Failed to read rotamer probability table for GLN Failed to open /usr/share/coot/rama-data/rota500-gln.data Failed to read rotamer probability table for ARG Failed to open /usr/share/coot/rama-data/rota500-arg.data Failed to read rotamer probability table for LYS Failed to open /usr/share/coot/rama-data/rota500-lys.data PROBLEM in coordinates file? failed to find all atoms in ich number 0 THR 16 A failure rotamer test: ("A" 1 "" 0.0 "Rotamer not recognised") ("A" 2 "" 0.0 "Rotamer not recognised") ("A" 16 "" 0.0 "Missing Atoms") FAIL: Rotamer outliers Entered testcase - Alt Conf Occ Sum Reset (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/res098.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/res098.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/res098.pdb has been read. Spacegroup: P 41 21 2 Cell: 57.374 57.374 87.384 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 11 read successfully For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 regularize: molecule 11 atom index 4 to 4 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 3 residues selected for refined and flanking residues created 6 bond restraints created 6 angle restraints created 0 plane restraints created 1 chiral vol restraints created 13 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 15 and 15 of chain X Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links INFO:: made 18 non-bonded restraints initial distortion_score: 8.98705 Initial Chi Squareds bonds: 0.149289 angles: 0.205078 torsions: N/A planes: 1.32634 non-bonded: 0 chiral vol: 0.0264636 rama plot: N/A Minimum found (iteration number 45) at 6.27253 Final Chi Squareds bonds: 0.00356353 angles: 0.290317 torsions: N/A planes: 0.654376 non-bonded: 0 chiral vol: 0.142707 rama plot: N/A SUCCESS TIME:: (dragged refinement): 9.08 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_res098.pdb_Thu_Sep_10_13:00:07_2009_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... For atom " CE " "A" returning occ 0.699999988079071 For atom " CE " "B" returning occ 0.200000002980232 For atom " NZ " "A" returning occ 0.699999988079071 For atom " NZ " "B" returning occ 0.200000002980232 test for closeness: 1.79999998211861 1.79999998211861 Entered testcase - Pepflip flips the correct alt confed atoms (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-pepflip-test.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-pepflip-test.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-pepflip-test.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 12 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_alt-conf-pepflip-test.pdb_Thu_Sep_10_13:00:08_2009_modification_0.pdb.gz flipped 65 A Entered testcase - Correction of CISPEP test (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern-cis-pep-12A_refmac0.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 13 read successfully (go-to-view-number 1 1) omega: 1 12.7704 degrees INFO This is a CIS peptide - making it TRANS INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_13:00:08_2009_modification_0.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_13:00:08_2009_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 11 A 12 flipped 11 A INFO:: mutate 11 A to a GLY INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_13:00:08_2009_modification_2.pdb.gz (mutate 11 "A" 13 "GLY") DEBUG:: check_dictionary_for_residues returns OK! INFO:: 4 residues selected for refined and flanking residues created 10 bond restraints created 10 angle restraints created 0 plane restraints created 1 chiral vol restraints created 21 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links INFO:: made 62 non-bonded restraints initial distortion_score: 565.206 Initial Chi Squareds bonds: 237.864 angles: 54.5685 torsions: N/A planes: 7.86923 non-bonded: 1.84407 chiral vol: 9.26976 rama plot: N/A Minimum found (iteration number 18) at -4818.58 Final Chi Squareds bonds: 1.04822 angles: 0.764573 torsions: N/A planes: 5.75545 non-bonded: 0 chiral vol: 0.00533487 rama plot: N/A SUCCESS TIME:: (dragged refinement): 10.082 Refinement elapsed time: 0.103 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_13:00:08_2009_modification_3.pdb.gz INFO:: replace_coords: 11 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... INFO:: mutate 11 A to a LEU INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_13:00:08_2009_modification_4.pdb.gz (mutate 11 "A" 13 "LEU") ==== fitting residue 11 of chain A to map number 2 ====== INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_13:00:08_2009_modification_5.pdb.gz INFO:: replace_coords: 8 atoms updated. Fitting score for best rotamer: 8.41928 (auto-fit-best-rotamer 11 "" "" "A" 13 2 1 1) DEBUG:: check_dictionary_for_residues returns OK! INFO:: 4 residues selected for refined and flanking residues created 14 bond restraints created 16 angle restraints created 0 plane restraints created 2 chiral vol restraints created 32 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 11 and 12 of chain A Link restraints: 1 bond links 3 angle links 2 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links INFO:: made 142 non-bonded restraints initial distortion_score: -6001 Initial Chi Squareds bonds: 1.01589 angles: 1.19474 torsions: N/A planes: 9.04357 non-bonded: 0 chiral vol: 0.00822091 rama plot: N/A Minimum found (iteration number 49) at -6078.09 Final Chi Squareds bonds: 1.1612 angles: 0.603749 torsions: N/A planes: 5.93809 non-bonded: 0 chiral vol: 0.297033 rama plot: N/A SUCCESS TIME:: (dragged refinement): 10.574 Refinement elapsed time: 0.106 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern-cis-pep-12A_refmac0.pdb_Thu_Sep_10_13:00:08_2009_modification_6.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... (write-pdb-file 13 "tmp-fixed-cis.pdb") /bin/grep CISPEPs: "3" Entered testcase - Refine Zone with Alt conf (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 14 read successfully (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.071 seconds to read MTZ file INFO:: 0.003 seconds to initialize map INFO:: 0.1 seconds for FFT INFO:: 0.011 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.067 seconds for contour map INFO:: 0.252 seconds in total DEBUG:: check_dictionary_for_residues returns OK! INFO:: 3 residues selected for refined and flanking residues created 5 bond restraints created 4 angle restraints created 0 plane restraints created 1 chiral vol restraints created 10 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 72 and 72 of chain B Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 2 residues (flanking restraints) Flanking residue restraints: 2 bond links 6 angle links 4 plane links INFO:: made 12 non-bonded restraints initial distortion_score: -2784.62 Initial Chi Squareds bonds: 1.62991 angles: 1.14414 torsions: N/A planes: 0.831346 non-bonded: 0 chiral vol: 2.13751 rama plot: N/A Minimum found (iteration number 16) at -3085.72 Final Chi Squareds bonds: 2.46124 angles: 3.87881 torsions: N/A planes: 3.80237 non-bonded: 0.00908571 chiral vol: 4.58403 rama plot: N/A SUCCESS TIME:: (dragged refinement): 11.533 Refinement elapsed time: 0.048 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:10_2009_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... refined moved: d=0.595344045565208 Entered testcase - Sphere Refine (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-add-terminal-1-test.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 83/90 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 16 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-add-terminal-1-test.pdb_Thu_Sep_10_13:00:10_2009_modification_0.pdb.gz (set-go-to-atom-molecule 16) imol: 16 residues: (("A" 93 "") ("A" 5 "") ("A" 3 "") ("A" 92 "")) DEUBG:: There are 64 atoms total (including flankers) created 27 bond restraints created 31 angle restraints created 1 plane restraints created 5 chiral vol restraints created 64 restraints INFO:: [spec: "A" 93 ""] [spec: "A" 92 ""] link_type :TRANS: Link restraints: 1 bond links 3 angle links 2 plane links Flanking residue restraints: 5 bond links 15 angle links 10 plane links INFO:: made 676 non-bonded restraints initial distortion_score: -15808.7 Initial Chi Squareds bonds: 1.8196 angles: 1.27384 torsions: N/A planes: 1.01372 non-bonded: 0 chiral vol: 0.658962 rama plot: N/A Minimum found (iteration number 44) at -16083.9 Final Chi Squareds bonds: 1.57653 angles: 0.571875 torsions: N/A planes: 0.762081 non-bonded: 0 chiral vol: 0.104681 rama plot: N/A SUCCESS TIME:: (dragged refinement): 12.543 Entered testcase - Rigid Body Refine Alt Conf Waters (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-waters.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-waters.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/alt-conf-waters.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 17 read successfully masking....masking done INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_alt-conf-waters.pdb_Thu_Sep_10_13:00:11_2009_modification_0.pdb.gz INFO:: replace_coords: 1 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... WARNING:: refine_zone: Can't get index for resno1: 2 ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - Setting multiple atom attributes Entered testcase - Tweak Alt Confs on Active Residue (set-go-to-atom-molecule 0) (set-atom-string-attribute 0 "B" 58 "" " CB " "" "alt-conf" "B") Entered testcase - Backrub rotamer (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/backrub-fragment.pdb" 0) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/backrub-fragment.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/backrub-fragment.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 18 read successfully Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 18) INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_backrub-fragment.pdb_Thu_Sep_10_13:00:12_2009_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_backrub-fragment.pdb_Thu_Sep_10_13:00:12_2009_modification_1.pdb.gz INFO:: replace_coords: 14 atoms updated. Entered testcase - Libcif horne (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/coords-B3A.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/coords-B3A.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/coords-B3A.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 20 read successfully regularize: molecule 20 atom index 0 to 0 DEUBG:: check_dictionary_for_residues - problem... WARNING:: Failed to find restraints for :B3A: INFO:: 1 residues selected for refined and flanking residues created 0 bond restraints created 0 angle restraints created 0 plane restraints created 0 chiral vol restraints created 0 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links No restraints: regularize() ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... WARNING: in init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/lib-B3A.cif not found. init_refmac_mon_lib /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/lib-B3A.cif had no bond restraints regularize: molecule 20 atom index 0 to 0 DEUBG:: check_dictionary_for_residues - problem... WARNING:: Failed to find restraints for :B3A: INFO:: 1 residues selected for refined and flanking residues created 0 bond restraints created 0 angle restraints created 0 plane restraints created 0 chiral vol restraints created 0 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links No restraints: regularize() ------------ ERROR! ------------------- moving_atoms_asc_type not known: 0 ------------ ERROR! ------------------- INFO:: graphics_info_t::clear_up_moving_atoms... WARNING:: attempting to delete NULL moving_atoms_asc.atom_selection Ignoring. attempting to delete NULL moving_atoms_asc.mol ignoring DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... There are 3 data in /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/lib-both.cif Read 28 atoms/links in restraints from /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/lib-both.cif regularize: molecule 20 atom index 0 to 0 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 5 bond restraints created 5 angle restraints created 0 plane restraints created 1 chiral vol restraints created 11 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 10 non-bonded restraints initial distortion_score: 0.00371314 Initial Chi Squareds bonds: 0.00061433 angles: 0.000126593 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 8.51661e-06 rama plot: N/A Minimum found (iteration number 6) at 3.86343e-05 Final Chi Squareds bonds: 1.20485e-07 angles: 7.25441e-06 torsions: N/A planes: N/A non-bonded: 0 chiral vol: 1.75988e-06 rama plot: N/A SUCCESS TIME:: (dragged refinement): 14.331 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_coords-B3A.pdb_Thu_Sep_10_13:00:13_2009_modification_0.pdb.gz INFO:: replace_coords: 6 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - Refmac Parameters Storage (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "/RNASE3GMP/COMPLEX/FWT" "/RNASE3GMP/COMPLEX/PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.106 seconds to read MTZ file INFO:: 0.004 seconds to initialize map INFO:: 0.187 seconds for FFT INFO:: 0.015 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.071 seconds for contour map INFO:: 0.383 seconds in total INFO:: Stored refmac parameters: /RNASE3GMP/COMPLEX/FGMP18 /RNASE3GMP/COMPLEX/SIGFGMP18 /RNASE/NATIVE/FreeR_flag is sensible. Entered testcase - OXT is added before TER record - add only one (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/test-TER-OXT.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/test-TER-OXT.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/test-TER-OXT.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 22 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_test-TER-OXT.pdb_Thu_Sep_10_13:00:13_2009_modification_0.pdb.gz Added OXT at 1/A/14/ASP/ OXT altLoc :: segid :: pos: (33.1294,-9.08972,14.9163) B-factor: 45 (add-OXT-to-residue 22 14 "" "A") WARNING:: This residue already has an OXT - aborting (add-OXT-to-residue 22 14 "" "A") (write-pdb-file 22 "test-TER-OXT-added.pdb") found TER "TER 25 ASP A 14 " Entered testcase - The position of the oxygen after a mutation (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/val.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/val.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/val.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 23 read successfully INFO:: mutate 3 C to a HIS INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_val.pdb_Thu_Sep_10_13:00:14_2009_modification_0.pdb.gz (mutate 3 "C" 23 "HIS") (write-pdb-file 23 "his.pdb") Entered testcase - Deleting (non-existing) Alt conf and Go To Atom [JED] failed to delete residue atoms A 88 :A: (delete-residue-with-altconf 0 "A" 88 "" "A") Entered testcase - Mask and difference map (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.057 seconds to read MTZ file INFO:: 0.006 seconds to initialize map INFO:: 0.083 seconds for FFT INFO:: 0.012 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.033 seconds for contour map INFO:: 0.191 seconds in total (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.2 INFO grid sampling...Nuvw = ( 160, 192, 96) INFO:: 0.051 seconds to read MTZ file INFO:: 0.193 seconds to initialize map INFO:: 0.185 seconds for FFT INFO:: 0.02 seconds for statistics Map mean: ........ 1.18834e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.05176 Map minimum: ..... -0.921659 INFO:: 0.08 seconds for contour map INFO:: 0.529 seconds in total (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 0) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 26 read successfully INFO:: Masking around 64 atoms Map statistics: mean: -0.00140323 st.d: 0.305597 Map statistics: min: -0.875045, max: 2.97757 -0.77873 55 -0.586099 2468 -0.393468 24912 -0.200837 59810 -0.00820671 81565 0.184424 31729 0.377055 10140 0.569685 6763 0.762316 4842 0.954947 3073 1.14758 1603 1.34021 726 1.53284 283 1.72547 93 1.9181 24 2.11073 3 2.30336 5 2.49599 1 2.68862 0 2.88125 1 3.07389 0 (atom-info-string 26 "A" 20 "" " CA " "") (atom-info-string 26 "A" 21 "" " CA " "") (atom-info-string 26 "A" 22 "" " CA " "") (atom-info-string 26 "A" 23 "" " CA " "") (atom-info-string 26 "A" 24 "" " CA " "") (atom-info-string 26 "A" 25 "" " CA " "") (atom-info-string 26 "A" 26 "" " CA " "") (atom-info-string 26 "A" 27 "" " CA " "") (atom-info-string 26 "A" 28 "" " CA " "") (atom-info-string 26 "A" 29 "" " CA " "") (atom-info-string 26 "A" 30 "" " CA " "") (atom-info-string 26 "A" 1 "" " CA " "") (atom-info-string 26 "A" 2 "" " CA " "") (atom-info-string 26 "A" 3 "" " CA " "") (atom-info-string 26 "A" 4 "" " CA " "") (atom-info-string 26 "A" 5 "" " CA " "") (atom-info-string 26 "A" 6 "" " CA " "") (atom-info-string 26 "A" 7 "" " CA " "") (atom-info-string 26 "A" 8 "" " CA " "") (atom-info-string 26 "A" 9 "" " CA " "") (atom-info-string 26 "A" 10 "" " CA " "") high-values: (0.923012852668762 0.928160607814789 0.963148474693298 0.588746070861816 0.692066609859467 0.7519770860672 0.68085777759552 0.954908907413483 1.00084149837494 0.981854677200317 0.726146519184113) low values: (0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0) Map statistics: mean: -0.00140318 st.d: 0.0601239 Map statistics: min: -2.78832, max: 0.730463 -2.70035 2 -2.52441 2 -2.34847 2 -2.17253 1 -1.99659 3 -1.82065 2 -1.64471 8 -1.46877 10 -1.29283 37 -1.1169 76 -0.940957 122 -0.765018 193 -0.589079 261 -0.41314 329 -0.237201 473 -0.0612622 224025 0.114677 1297 0.290616 919 0.466554 308 0.642493 26 0.818432 0 diff-high-values: (0.00255923601798713 0.00100331113208085 0.00106650416273624 -0.00237782066687942 0.00169654644560069 7.11922300979495e-4 0.00212939688935876 0.00194922799710184 0.00229486566968262 6.56027928926051e-4 0.00835366826504469) diff-low-values: (-0.887997150421143 -0.79390150308609 -1.18933141231537 -1.06666219234467 -0.988452911376953 -0.759092688560486 -0.748683869838715 -0.650666296482086 -0.904519736766815 -0.545242130756378) Entered testcase - Simple Averaged maps (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 108, 132, 64) INFO:: 0.051 seconds to read MTZ file INFO:: 0.004 seconds to initialize map INFO:: 0.078 seconds for FFT INFO:: 0.011 seconds for statistics Map mean: ........ 1.21317e-09 Map sigma: ....... 0.311501 Map maximum: ..... 2.97757 Map minimum: ..... -0.875045 INFO:: 0.035 seconds for contour map INFO:: 0.179 seconds in total (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz" "FWT" "PHWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 2.5 INFO grid sampling...Nuvw = ( 180, 216, 108) INFO:: 0.051 seconds to read MTZ file INFO:: 0.277 seconds to initialize map INFO:: 0.261 seconds for FFT INFO:: 0.025 seconds for statistics Map mean: ........ 1.0992e-09 Map sigma: ....... 0.311501 Map maximum: ..... 3.07133 Map minimum: ..... -0.877519 INFO:: 0.099 seconds for contour map INFO:: 0.713 seconds in total Map statistics: mean: -4.27665e-07 st.d: 0.311072 Map statistics: min: -0.873369, max: 2.97503 -0.777159 58 -0.584739 2569 -0.392319 25676 -0.1999 61199 -0.00747969 77803 0.18494 32128 0.37736 10498 0.56978 7060 0.7622 5057 0.954619 3192 1.14704 1668 1.33946 756 1.53188 288 1.7243 102 1.91672 25 2.10914 4 2.30156 7 2.49398 3 2.6864 1 2.87882 1 3.07124 1 Map statistics: mean: 4.28879e-07 st.d: 0.00106883 Map statistics: min: -0.00685638, max: 0.0119245 -0.00638686 26 -0.00544782 84 -0.00450877 335 -0.00356973 1277 -0.00263068 4286 -0.00169164 14039 -0.000752594 59649 0.000186451 105523 0.0011255 30405 0.00206454 7562 0.00300358 2850 0.00394263 1180 0.00488167 486 0.00582072 253 0.00675976 93 0.00769881 28 0.00863785 13 0.00957689 4 0.0105159 2 0.011455 1 0.012394 0 INFO:: map sigmas: normal 0.311072051525116 and diff-map: 0.00106883211992681 Entered testcase - Make a glycosidic linkage (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/multi-carbo-coot-2.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/multi-carbo-coot-2.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/multi-carbo-coot-2.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 33 read successfully bond-length: 2.97694066606539: regularize: molecule 33 atom index 0 to 20 There are 2 data in /usr/share/ccp4//data/monomers/f/FUC-A-L.cif There are 2 data in /usr/share/ccp4//data/monomers/n/NAG-B-D.cif DEBUG:: check_dictionary_for_residues returns OK! INFO:: 2 residues selected for refined and flanking residues created 46 bond restraints created 71 angle restraints created 1 plane restraints created 8 chiral vol restraints created 126 restraints INFO:: GetSelIndex (make_link_restraints) returned 2 residues (for link restraints) between (and including) residues 1 and 2 of chain A INFO:: glycosidic_linkage type :BETA1-4: INFO:: No chem link for groups L-pyranose D-pyranose and comp_ids FUC NAG Link restraints: 1 bond links 3 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 1560 non-bonded restraints initial distortion_score: 6392.77 Initial Chi Squareds bonds: 127.526 angles: 4.95566 torsions: N/A planes: 0.00816956 non-bonded: 0.0150013 chiral vol: 1.112 rama plot: N/A Minimum found (iteration number 163) at 246.274 Final Chi Squareds bonds: 1.72108 angles: 1.79956 torsions: N/A planes: 0.00103315 non-bonded: 0.014916 chiral vol: 1.11826 rama plot: N/A SUCCESS TIME:: (dragged refinement): 22.177 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_multi-carbo-coot-2.pdb_Thu_Sep_10_13:00:20_2009_modification_0.pdb.gz INFO:: replace_coords: 46 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... bond-length: 1.4403851227776: Entered testcase - Test for flying hydrogens on undo (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-VAL.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-VAL.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-VAL.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 34 read successfully regularize: molecule 34 atom index 0 to 0 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 132 non-bonded restraints initial distortion_score: 35.0317 Initial Chi Squareds bonds: 0.268606 angles: 0.0269163 torsions: N/A planes: N/A non-bonded: 0.230261 chiral vol: 0.20393 rama plot: N/A Minimum found (iteration number 10) at 0.247096 Final Chi Squareds bonds: 0.00015527 angles: 0.00897939 torsions: N/A planes: N/A non-bonded: 1.53575e-09 chiral vol: 0.0204374 rama plot: N/A SUCCESS TIME:: (dragged refinement): 22.847 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_13:00:21_2009_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... INFO:: undo molecule number set to: 34 (set-undo-molecule 34) INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_13:00:21_2009_modification_1.pdb.gz restoring from backup 2 2 Reading coordinate file: coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_13:00:21_2009_modification_0.pdb.gz PDB file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_13:00:21_2009_modification_0.pdb.gz has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule DEBUG:: apply_undo: (end) history_index: 0 max_history_index: 2 (apply-undo) regularize: molecule 34 atom index 0 to 0 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 14 bond restraints created 25 angle restraints created 0 plane restraints created 1 chiral vol restraints created 40 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 132 non-bonded restraints initial distortion_score: 35.0317 Initial Chi Squareds bonds: 0.268606 angles: 0.0269163 torsions: N/A planes: N/A non-bonded: 0.230261 chiral vol: 0.20393 rama plot: N/A Minimum found (iteration number 10) at 0.247096 Final Chi Squareds bonds: 0.00015527 angles: 0.00897939 torsions: N/A planes: N/A non-bonded: 1.53575e-09 chiral vol: 0.0204374 rama plot: N/A SUCCESS TIME:: (dragged refinement): 23.013 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-VAL.pdb_Thu_Sep_10_13:00:21_2009_modification_0.pdb.gz INFO:: replace_coords: 15 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - Test for mangling of hydrogen names from a PDB v 3.0 (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3ins-6B-3.0.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3ins-6B-3.0.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3ins-6B-3.0.pdb has been read. No Spacegroup found for this PDB file Cell: 1 1 1 90 90 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 35 read successfully regularize: molecule 35 atom index 0 to 0 DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues Unknown element : D: created 16 bond restraints created 28 angle restraints created 0 plane restraints created 1 chiral vol restraints created 45 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 6 and 6 of chain B Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 254 non-bonded restraints initial distortion_score: 20907.8 Initial Chi Squareds bonds: 31.4514 angles: 12.6131 torsions: N/A planes: N/A non-bonded: 78.9403 chiral vol: 0.567548 rama plot: N/A Minimum found (iteration number 26) at 0.252086 Final Chi Squareds bonds: 0.000107256 angles: 0.00825211 torsions: N/A planes: N/A non-bonded: 5.06464e-08 chiral vol: 0.0192984 rama plot: N/A SUCCESS TIME:: (dragged refinement): 23.982 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_3ins-6B-3.0.pdb_Thu_Sep_10_13:00:22_2009_modification_0.pdb.gz INFO:: replace_coords: 19 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - update monomer restraints In new_molecule_by_atom_selection has contains chain id A Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 11 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 28 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 78 non-bonded restraints initial distortion_score: -1120.52 Initial Chi Squareds bonds: 1.16837 angles: 0.718389 torsions: N/A planes: 9.33775 non-bonded: 40.0438 chiral vol: 0.995302 rama plot: N/A Minimum found (iteration number 48) at -4202.57 Final Chi Squareds bonds: 5.00835 angles: 0.722604 torsions: N/A planes: 0.917534 non-bonded: 0.0786912 chiral vol: 0.995449 rama plot: N/A SUCCESS TIME:: (dragged refinement): 24.08 Refinement elapsed time: 0.045 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_13:00:22_2009_modification_0.pdb.gz INFO:: replace_coords: 12 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Bond-length: 2.26496220633885: pass intermediate 2.8 tolerance test DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 12 bond restraints created 15 angle restraints created 1 plane restraints created 1 chiral vol restraints created 29 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 30 and 30 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 74 non-bonded restraints initial distortion_score: -3037.32 Initial Chi Squareds bonds: 102.207 angles: 0.722604 torsions: N/A planes: 0.917534 non-bonded: 0 chiral vol: 0.995449 rama plot: N/A Minimum found (iteration number 49) at -4306.6 Final Chi Squareds bonds: 1.22279 angles: 0.808124 torsions: N/A planes: 2.56077 non-bonded: 0 chiral vol: 0.995579 rama plot: N/A SUCCESS TIME:: (dragged refinement): 24.157 Refinement elapsed time: 0.046 INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_13:00:22_2009_modification_1.pdb.gz INFO:: replace_coords: 12 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... OK plane atom " CB " Bond-length: 1.53218859531565: Entered testcase - Refinement OK with zero bond esd (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-ACT.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-ACT.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/monomer-ACT.pdb has been read. Spacegroup: P 1 Cell: 100 100 100 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 37 read successfully There are 2 data in /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_ACT.cif Read 7 atoms/links in restraints from /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/libcheck_ACT.cif DEBUG:: check_dictionary_for_residues returns OK! INFO:: 1 residues selected for refined and flanking residues created 6 bond restraints created 9 angle restraints created 1 plane restraints created 0 chiral vol restraints created 15 restraints INFO:: GetSelIndex (make_link_restraints) returned 1 residues (for link restraints) between (and including) residues 1 and 1 of chain A Link restraints: 0 bond links 0 angle links 0 plane links INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 0 residues (flanking restraints) INFO:: GetSelIndex (make_flanking_atoms_restraints) returned 1 residues (flanking restraints) Flanking residue restraints: 0 bond links 0 angle links 0 plane links INFO:: made 0 non-bonded restraints initial distortion_score: 108.409 Initial Chi Squareds bonds: 0.00014374 angles: 4.27673e-05 torsions: N/A planes: 0 non-bonded: N/A chiral vol: N/A rama plot: N/A Minimum found (iteration number 66) at -1093.91 Final Chi Squareds bonds: 0.23613 angles: 0.64763 torsions: N/A planes: 0.000243983 non-bonded: N/A chiral vol: N/A rama plot: N/A SUCCESS TIME:: (dragged refinement): 24.858 Refinement elapsed time: 0.071 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_monomer-ACT.pdb_Thu_Sep_10_13:00:23_2009_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. INFO:: graphics_info_t::clear_up_moving_atoms... DEBUG:: in safe_python_command_with_return() pValue is 0x83ebbec clearing intermediate object... Entered testcase - Change Chain IDs and Chain Sorting (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 38 read successfully INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_0.pdb.gz istat: ; 1 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_1.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_2.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_3.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_4.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_5.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_6.pdb.gz INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_7.pdb.gz (n-chains 38) (chain_id 38 0) (chain_id 38 1) (chain_id 38 2) (chain_id 38 3) (chain_id 38 4) (chain_id 38 5) (chain_id 38 6) (chain_id 38 7) (chain_id 38 8) Entered testcase - Replace Fragment Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) (copy-molecule 0) In new_molecule_by_atom_selection has contains chain id A In new_molecule_by_atom_selection has contains chain id B Symmetry available for this molecule (update-go-to-atom-window-on-new-mol) INFO:: backup file coot-backup/atom_selection_from_tutorial-modern.pdb_Thu_Sep_10_13:00:24_2009_modification_0.pdb.gz INFO:: backup file coot-backup/Copy_of__var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:25_2009_modification_0.pdb.gz INFO:: replace_coords: 1465 atoms updated. (replace-fragement 39 "//A70-80") distances: (20.8326663813327 20.8326666331108 20.8326661982214 20.8326666331108 20.8326663813327) Entered testcase - Residues in Region of Residue found 6 neighbours (("B" 60 "") ("A" 42 "") ("B" 61 "") ("A" 38 "") ("A" 41 "") ("A" 39 "")) found 0 neighbours () Entered testcase - Residues in region of a point (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 41 read successfully Entered testcase - Empty molecule on type selection in new_molecule_by_residue_type_selection Something bad happened - No residues selected (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") in new_molecule_by_residue_type_selection Something bad happened - No residues selected (info-dialog "Oops, failed to select residue type. No residues selected Residue "TRP" does not exist in molecule 0!?") Entered testcase - Set Rotamer INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_tutorial-modern.pdb_Thu_Sep_10_13:00:25_2009_modification_0.pdb.gz oops! in rotamer::GetResidue() No tree in restraint oops! in rotamer::GetResidue() No tree in restraint Entered testcase - Rotamer names and scores are correct (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 42 read successfully (backup-state 42) (turn-off-backup 42) (rotamer-score 42 "A" 28 "") Rotamer 0 : "m-85" 44.0 fail on rotamer probability: result: 44.0 should be: 100 FAIL: Rotamer names and scores are correct Entered testcase - Align and mutate a model with deletions (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb has been read. Spacegroup: P 21 21 21 Cell: 64.897 78.323 38.792 90 90 90 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 50/87 Molecule 43 read successfully INFO:: aligning to mol number 43chain: A ------------------------------------------------- chain A ------------------------------------------------- INFO:: input model sequence:GTVCLSAEATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVITARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: input target sequence:DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID > /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/rnase-A-needs-an-insertion.pdb ---GTVCLSA---EATDTLNLIAASDGPFPYSSQDGVVFQNRESVLPTQSYGYYHEYTVIT--ARTRGTRRIICGEATQEDYYTGDHYATFSLID > target seq: DVSGTVCLSALPPEATDTLNLIA-SDGPFPYS-QDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIICGEATQEDYYTGDHYATFSLID INFO:: alignment score 160 There are 8 single_insertions INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_rnase-A-needs-an-insertion.pdb_Thu_Sep_10_13:00:27_2009_modification_0.pdb.gz INFO:: Removing CIS peptide from PDB header: A 26 A 27 The alignment resulted in the following Insertions (coalesced): from 1 to 4 ASP VAL SER from 11 to 14 LEU PRO PRO from 62 to 64 PRO GLY Insertions (singles): [spec: "A" 1 ""] -> ASP [spec: "A" 2 ""] -> VAL [spec: "A" 3 ""] -> SER [spec: "A" 11 ""] -> LEU [spec: "A" 12 ""] -> PRO [spec: "A" 13 ""] -> PRO [spec: "A" 62 ""] -> PRO [spec: "A" 63 ""] -> GLY Deletions: [spec: "A" 24 ""] [spec: "A" 33 ""] Mutations: apply resno updates... Applied 3 insertions Applied 0 mutations Applied 2 deletions (write-pdb-file 43 "mutated.pdb") ::::: (43 "A" 1 "") #f #f ::::: (43 "A" 4 "") #t #t ::::: (43 "A" 59 "") #t #t ::::: (43 "A" 60 "") #f #f ::::: (43 "A" 61 "") #f #f ::::: (43 "A" 92 "") #t #t ::::: (43 "A" 94 "") #f #f Entered testcase - Autofit Rotamer on Residues with Insertion codes (handle-read-draw-molecule-with-recentre "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb3hfl.ent" 1) Reading coordinate file: /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb3hfl.ent PDB file /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/pdb3hfl.ent has been read. No Spacegroup found for this PDB file Cell: 54.79 74.82 78.95 90 101.82 90 INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model INFO:: NCS chain comparison 15/212 INFO:: NCS chain comparison 7/212 INFO:: NCS chain comparison 10/215 Molecule 44 read successfully (make-and-draw-map "/var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) INFO:: making map from mtz filename /var/tmp/portage/sci-chemistry/coot-9999/work/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.5 INFO grid sampling...Nuvw = ( 64, 96, 90) INFO:: 0.066 seconds to read MTZ file INFO:: 0.004 seconds to initialize map INFO:: 0.1 seconds for FFT INFO:: 0.039 seconds for statistics Map mean: ........ 3.31773e-12 Map sigma: ....... 0.260405 Map maximum: ..... 1.71787 Map minimum: ..... -1.03389 INFO:: 0.017 seconds for contour map INFO:: 0.226 seconds in total ==== fitting residue 52A of chain H to map number 45 ====== INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb3hfl.ent_Thu_Sep_10_13:00:28_2009_modification_0.pdb.gz INFO:: replace_coords: 7 atoms updated. Fitting score for best rotamer: 5.82781 (auto-fit-best-rotamer 52 "" "A" "H" 44 45 0 0) INFO:: backup file coot-backup/_var_tmp_portage_sci-chemistry_coot-9999_work_data_greg-data_pdb3hfl.ent_Thu_Sep_10_13:00:28_2009_modification_1.pdb.gz Entered testcase - RNA base has correct residue type after mutation INFO:: 5 matched atoms had: mean devi: 0 rms devi: 0