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 computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
