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): 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 >
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