Dear Spencer

It is possible to work this out using the PDBe API. 
for our interactive API see:

The molecules url will give you this information:

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

The images are made with pymol (currently 1.6, but also works in 1.7)



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
> through
> 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
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD UK
Tel: +44 1223 492529
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