[Chimera-users] Scripting headless Chimera

[gregc at cgl.ucsf.edu]

To change the window size in both the headless and the regular chimera,
use the windowsize command.

   -- Greg

> Hi Mark,
>
>    The error message says your script tried to open a file with the
> "open" Chimera command and that file does not exist.  If you get the
> first image I guess your path to the directory must be ok. Not sure why
> your second file is not found.  I guess I'd need to see both the script
> and a listing of the directory with the files to understand it.
>
>    As for saving images, the Mac version is going to use the screen
> dimensions of the graphics window when saving an image if you don't
> specify the image size.  The headless Linux version has no window so I
> don't know what the default would be.  You should specify the image size
> in the image saving command.
>
>      Tom
>
>
>
>> Hello,
>>
>> 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>
>>      callChimera(data[ab][4],data[ab][5],fn,dn)
>>    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.
>>
>> -Mark
>>
>> -This e-mail and any attachments may contain CONFIDENTIAL information,
>> including PROTECTED HEALTH INFORMATION. If you are not the intended
>> recipient, any use or disclosure of this information is STRICTLY
>> PROHIBITED; you are requested to delete this e-mail and any attachments,
>> notify the sender immediately, and notify the LabCorp Privacy Officer at
>> privacyofficer at labcorp.com or call (877) 23-HIPAA / (877) 234-4722.
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>