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): 0x00007f11f8744f40 *** > > > > 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
