[PyMOL] Pymol crash when raytracing empty graphics
We have a pipeline that uses pymol to create images using the headless command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at least) crash if you try to ray-trace an empty viewport. Example: pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray' This particular example only has CA atoms, so the cartoon mode doesn't show anything. In interactive mode I would `set cartoon_trace_atoms,1` but when batch processing there isn't a good way of detecting whether anything is showing or not. The error is: *** glibc detected *** /home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or corruption (out): 0x7f11f8744f40 *** I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL 1.7.4.1 through 1.7.6.3. Attached is a stack trace. Any suggestions on ensuring that there are some polygons in frame would also be appreciated. Say, if there was a way to detect that cartoon would fail so that I can switch to a lines or nonbonded representation (I wish that was the default fallback for cartoon). Thanks, Spencer pymol_crash.log Description: Binary data -- ___ 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
Re: [PyMOL] Pymol crash when raytracing empty graphics
Dear Spencer It is possible to work this out using the PDBe API. for our interactive API see: http://www.ebi.ac.uk/pdbe/api/doc/ The molecules url will give you this information: http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q entity 1 has ca_p_only: true, which means cartoon will not work for this chain - so we use ribbon instead with the command pymol.cmd.set(ribbon_trace_atoms, 1) This test allows us to make images such as those shown on the entry page for 1a1q at PDBe http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q The images are made with pymol (currently 1.6, but also works in 1.7) Regards John PDBe On Monday 17 August 2015 15:40:14 Spencer Bliven wrote: We have a pipeline that uses pymol to create images using the headless command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at least) crash if you try to ray-trace an empty viewport. Example: pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray' This particular example only has CA atoms, so the cartoon mode doesn't show anything. In interactive mode I would `set cartoon_trace_atoms,1` but when batch processing there isn't a good way of detecting whether anything is showing or not. The error is: *** glibc detected *** /home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or corruption (out): 0x7f11f8744f40 *** I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL 1.7.4.1 through 1.7.6.3. Attached is a stack trace. Any suggestions on ensuring that there are some polygons in frame would also be appreciated. Say, if there was a way to detect that cartoon would fail so that I can switch to a lines or nonbonded representation (I wish that was the default fallback for cartoon). Thanks, Spencer -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 -- ___ 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
Re: [PyMOL] .pdb files and rendering software
Hi again, Joe - Try saving in COLLADAhttp://www.pymolwiki.org/index.php/COLLADA format with `save myfile.dae` (in PyMOL v1.7.3.2 or later). If you're using Blender, you'll need to `set collada_geometry_mode, 1`, because Blender only supports polylists for COLLADA import, and not the more efficient structures like triangles, tristrips, trifans, etc. I've never used Maya, so I'm not sure if it has any peculiarities in its COLLADA support. There is also VRML2, which you can get with `save myfile.wrl`, but I'm partial to the COLLADA exporter, since I wrote it. ;) Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Aug 15, 2015, at 1:42 PM, Joseph Georgeson joseph.george...@weizmann.ac.ilmailto:joseph.george...@weizmann.ac.il wrote: Hi all, I was wondering the best options for importing .pdb files into rendering programs like Maya or Blender. Right now I'm trying mMaya with Maya2014 but seem to have many issues. Any suggestions? Thanks, JoeG -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- ___ 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
Re: [PyMOL] How does PyMOL create .obj file?
Hi Joe - The coordinate system in the .obj file is in camera space, where (0,0,0) is the center of the viewport, positive x to the right, positive y up, and positive z out of the screen toward the viewer. If you want to correlate them, you would need to transform the model coordinates using the view matrix or, probably more easily, set the view to coincide with model space, as specified under Space and File saving herehttp://www.pymolwiki.org/index.php/Model_Space_and_Camera_Space. FYI, there is a bughttps://sourceforge.net/p/pymol/bugs/170/ in .obj output of spheres, which are output as a single triangle face with identical coordinates for all three points. Needless to say, you can't see them, unless you zoom in really close. Also, cylinders and cones are not yet implemented in .obj output, so, basically the only representation fully supported is surfaces, which are made entirely of triangle meshes. Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Aug 15, 2015, at 1:34 PM, Joseph Georgeson joseph.george...@weizmann.ac.ilmailto:joseph.george...@weizmann.ac.il wrote: Hi all, I'm trying to correlate an .obj file created in PyMOL to the actual molecular coordinates of a protein from the .pdb file. Is this possible? Does anyone know how PyMOL creates the .obj file? Thanks, JoeG -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. = -- ___ 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
Re: [PyMOL] Pymol crash when raytracing empty graphics
Hi Spencer, Thank you for the bug report. We could reproduce and fix the crash, if you want I can send you a hotfix build. I will also push the fix to the open source SVN repository soon. I second John's suggestions to query the ca_p_only property from the PDBe API. Also, the next PyMOL version will read that property from the mmCIF file and automatically set the cartoon_trace_atoms and ribbon_trace_atoms settings. Cheers, Thomas On 17 Aug 2015, at 10:58, John Berrisford j...@ebi.ac.uk wrote: Dear Spencer It is possible to work this out using the PDBe API. for our interactive API see: http://www.ebi.ac.uk/pdbe/api/doc/ The molecules url will give you this information: http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q entity 1 has ca_p_only: true, which means cartoon will not work for this chain - so we use ribbon instead with the command pymol.cmd.set(ribbon_trace_atoms, 1) This test allows us to make images such as those shown on the entry page for 1a1q at PDBe http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q The images are made with pymol (currently 1.6, but also works in 1.7) Regards John PDBe On Monday 17 August 2015 15:40:14 Spencer Bliven wrote: We have a pipeline that uses pymol to create images using the headless command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at least) crash if you try to ray-trace an empty viewport. Example: pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray' This particular example only has CA atoms, so the cartoon mode doesn't show anything. In interactive mode I would `set cartoon_trace_atoms,1` but when batch processing there isn't a good way of detecting whether anything is showing or not. The error is: *** glibc detected *** /home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or corruption (out): 0x7f11f8744f40 *** I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL 1.7.4.1 through 1.7.6.3. Attached is a stack trace. Any suggestions on ensuring that there are some polygons in frame would also be appreciated. Say, if there was a way to detect that cartoon would fail so that I can switch to a lines or nonbonded representation (I wish that was the default fallback for cartoon). Thanks, Spencer -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ 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
