[Chimera-users] Scripting headless Chimera

Evans, Mark Evansm8 at labcorp.com
Fri Jul 6 15:02:28 PDT 2012


I am doing some epitope analysis and I am generating images of each potential epitope overlaid and colored on the antigen model. I have a script that loops through a list of residue sets (epitopes) and uses chimera to generate the images.

The script works if I call it from within Chimera running on Mac OSX.  I just installed the headless version on Redhat linux and was trying to modify my python script to run on the headless version and I ran into a few issues I would like some advice with.

1. Say I have ten sets of residues, which should produce 10 images.  I get the first one, but then I get the following error:

Traceback (most recent call last):
  File "/opt/bin/Chimera64-1.6.2rc/share/chimeraInit.py", line 686, in init
    midas_text.doRunScript("runscript", script)
  File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 2037, in doRunScript
    execfile(scriptPath, scriptGlobals)
  File "batchEpitopeModel3.py", line 144, in <module>
  File "batchEpitopeModel3.py", line 29, in callChimera
    rc("open " + trimer)
  File "/opt/bin/Chimera64-1.6.2rc/share/chimera/__init__.py", line 2426, in runCommand
    makeCommand(*args, **kw)
  File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 69, in makeCommand
    f(c, args)
  File "/opt/bin/Chimera64-1.6.2rc/share/Midas/midas_text.py", line 1427, in doOpen
    modelArg, noprefs)
  File "<string>", line 1, in <module>
  File "/opt/bin/Chimera64-1.6.2rc/share/Midas/__init__.py", line 1937, in open
    raise MidasError('%s' % msg)
MidasError: No such file or directory

Error while processing 'batchEpitopeModel3.py':
MidasError: No such file or directory

  File "/opt/bin/Chimera64-1.6.2rc/share/Midas/__init__.py", line 1937, in open
    raise MidasError('%s' % msg)

It seems like Chimera terminated my script, even though it should be executing a loop.

2. The images that are generated on the Mac are large, hi-res pngs, but the images generated by the headless version are very small, low-res versions.  I am not setting any image dimensions, are the defaults different between the two versions?

Thanks for any help.  I can post (or email directly) part of my python code if that is helpful.


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