Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-18 Thread Spencer Bliven
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): 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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[PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread Spencer Bliven
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
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Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread John Berrisford
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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Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread Thomas Holder
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): 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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