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 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
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 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
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
[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