Re: [PyMOL] dcd trajectories in PyMOL
Hi Andreas, I forgot one step, sorry. The update.py script does not copy the header files from the include directory, so you need: cd $VMD/plugins/include cp vmdconio.h molfile_plugin.h $PYMOL/contrib/uiuc/plugins/include Here I put $VMD and $PYMOL as the respective source tree roots. Hopefully these were all steps now... Cheers, Thomas On 02/28/2012 07:39 PM, Andreas Förster wrote: Thanks for your help, Thomas, but this didn't do the trick for me. I can run the python update.py and get a list of available plugins, but python setup.py build install (after patching) still crashes at the point of compiling the VMD plugins. gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -Igenerated/include -Igenerated/src -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/include/python2.6 -c contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -ffast-math -funroll-loops -O3 -g In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:43: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘init_qmdata’: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error: ‘MOLFILE_QMSTATUS_UNKNOWN’ undeclared (first use in this function) contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error: (Each undeclared identifier is reported only once contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error: for each function it appears in.) contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function ‘read_basis_rundata’: contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:262: error: ‘molfile_qm_basis_t’ has no member named ‘shell_types’ error: command 'gcc' failed with exit status 1 Looks like I'm tied to VMD. Andreas On 28/02/2012 3:02, Thomas Holder wrote: Hi Andreas, this error was introduced in the open-source tree with the updates from PyMOL 1.5. I'm not sure what the easiest fix would be, but here is how I got it to work: Download the latest VMD source code and unpack it: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD In the PyMOL source tree, edit the file contrib/uiuc/plugins/molfile_plugin/update.py and point molfile_src_path to the correct path in the VMD source tree. Then run python update.py. In setup.py, comment out cpmdlogplugin.c, cpmdplugin.c and gaussianplugin.c (they are commented out in update.py as well). You may use the attached patch. Cheers, Thomas On 02/28/2012 11:36 AM, Andreas Förster wrote: Dear all, driven beyond the reach of sanity by VMD, I've tried to enable the loading of DCD trajectories (from NAMD2 molecular dynamics simulations) in PyMOL. I followed the instructions given on this mailing list a few weeks back, specifically (setup.py): - uncommenting contrib/uiuc/plugins/include, contrib/uiuc/plugins/molfile_plugin/src, (_PYMOL_VMD_PLUGINS,None), - changing the line underneath # VMD plugin support # switch the 0 to 1 to activate the additional source code from ] + 0 * [ to ] + 1 * [ Compilation (python setup.py build install) crashes because of an error in the molfile plugin: contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function ‘read_basis_metadata’: contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208: error: ‘molfile_qm_metadata_t’ has no member named ‘have_esp’ contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209: error: ‘molfile_qm_metadata_t’ has no member named ‘have_npa’ contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211: error: ‘molfile_qm_metadata_t’ has no member named ‘have_internals’ error: command 'gcc' failed with exit status 1 Have others encountered that? Is there a solution or work-around? Thanks. Andreas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud
Re: [PyMOL] dcd trajectories in PyMOL
Hi Andreas, this error was introduced in the open-source tree with the updates from PyMOL 1.5. I'm not sure what the easiest fix would be, but here is how I got it to work: Download the latest VMD source code and unpack it: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD In the PyMOL source tree, edit the file contrib/uiuc/plugins/molfile_plugin/update.py and point molfile_src_path to the correct path in the VMD source tree. Then run python update.py. In setup.py, comment out cpmdlogplugin.c, cpmdplugin.c and gaussianplugin.c (they are commented out in update.py as well). You may use the attached patch. Cheers, Thomas On 02/28/2012 11:36 AM, Andreas Förster wrote: Dear all, driven beyond the reach of sanity by VMD, I've tried to enable the loading of DCD trajectories (from NAMD2 molecular dynamics simulations) in PyMOL. I followed the instructions given on this mailing list a few weeks back, specifically (setup.py): - uncommenting contrib/uiuc/plugins/include, contrib/uiuc/plugins/molfile_plugin/src, (_PYMOL_VMD_PLUGINS,None), - changing the line underneath # VMD plugin support # switch the 0 to 1 to activate the additional source code from] + 0 * [ to ] + 1 * [ Compilation (python setup.py build install) crashes because of an error in the molfile plugin: contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function ‘read_basis_metadata’: contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208: error: ‘molfile_qm_metadata_t’ has no member named ‘have_esp’ contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209: error: ‘molfile_qm_metadata_t’ has no member named ‘have_npa’ contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211: error: ‘molfile_qm_metadata_t’ has no member named ‘have_internals’ error: command 'gcc' failed with exit status 1 Have others encountered that? Is there a solution or work-around? Thanks. Andreas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen Index: setup.py === --- setup.py (revision 3983) +++ setup.py (working copy) @@ -9,6 +9,8 @@ from distutils.core import setup, Extension import sys, os +with_vmd_plugins = 0 + # if sys.platform=='win32': # NOTE: this branch not tested in years and may not work... @@ -265,6 +267,11 @@ -g ] ext_link_args = [] +with_vmd_plugins = 1 +if with_vmd_plugins: +inc_dirs += [ contrib/uiuc/plugins/include, + contrib/uiuc/plugins/molfile_plugin/src] +def_macros += [ (_PYMOL_VMD_PLUGINS, None) ] distribution = setup ( # Distribution meta-data name = pymol, @@ -420,7 +427,7 @@ layer5/main.c # VMD plugin support # switch the 0 to 1 to activate the additional source code -] + 0 * [ +] + (1 if with_vmd_plugins else 0) * [ # (incomplete support -- only TRJ, TRR, XTC, DCD so far...) 'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c', 'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp', @@ -432,8 +439,8 @@ 'contrib/uiuc/plugins/molfile_plugin/src/carplugin.c', 'contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp', 'contrib/uiuc/plugins/molfile_plugin/src/corplugin.c', -'contrib/uiuc/plugins/molfile_plugin/src/cpmdlogplugin.c', -'contrib/uiuc/plugins/molfile_plugin/src/cpmdplugin.c', +#'contrib/uiuc/plugins/molfile_plugin/src/cpmdlogplugin.c', +#'contrib/uiuc/plugins/molfile_plugin/src/cpmdplugin.c', 'contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c', 'contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp', 'contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c', @@ -444,7 +451,7 @@ 'contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp', 'contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp', 'contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c', -'contrib/uiuc/plugins/molfile_plugin/src/gaussianplugin.c', +#'contrib/uiuc/plugins/molfile_plugin/src/gaussianplugin.c', 'contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp', 'contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp', 'contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp', -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,
