Re: [PyMOL] Pymol crash when raytracing empty graphics
Thanks for the quick fix! I would love to get a hotfix if possible. The PDBe API is a nice solution. I think that detecting CA traces will fix 90% of the cases. There are still a few edge cases besides CA which don't have a cartoon mode (e.g. 1hzs, which has a polydeoxyribonucleotide polymer type but lacks phosphate atoms needed for cartoon), but these are rare enough to be handled individually. -Spencer On Mon, Aug 17, 2015 at 7:54 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: 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 -- ___ 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] 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