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.
>
>
>
> --
> ___
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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.
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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
--
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[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
