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
------------------------------------------------------------------------------
_______________________________________________ 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
