[Chimera-users] Scripting headless Chimera

[Tom Goddard]

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
>
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