[Chimera-users] [External] import error from module: Togl

Greg Couch gregc at cgl.ucsf.edu
Fri Jul 25 10:18:55 PDT 2014


Chimera's Python is self-contained and should not be affected by 
automatic updates.  And the GUI versions of Chimera come with Togl.  But 
you are using the headless version of Chimera.  So the simple workaround 
is to use a GUI version of Chimera with your script.

The headless version *should* work, but historical and accidental 
dependencies on the GUI code sometimes prevent it from working. These 
should be reported as bugs.  The accidental dependencies, like it sounds 
like what happened to you, can and will be fixed. We will even fix the 
historical dependencies if they are not too hard to fix.

     HTH,

     Greg

On 07/25/2014 09:28 AM, Mike Sivley wrote:
> I apologize in advance if this becomes too system-specific, as I 
> believe an automatic update of our server's python libraries may be to 
> blame for this error. However, my hope is that others may have run 
> into the issue as well and have already found a solution.
>
> I have a python/chimera script that generates Chimera scenes with 
> various annotations assigned to residues in a protein structure. This 
> script worked without issue for several weeks. I returned from a week 
> of vacation and now the script fails with the following error:
>
> ImportError: No module named Togl
>
>   File 
> "/ant2/Bush_eQTL/sivleyrm/bin/UCSF-Chimera64-2014-05-13/share/chimera/tkgui.py", 
> line 73, in <module>
>     import Togl
>
> Togl appears to be a deprecated library, so my best guess is that it 
> was removed during some automatic update (possibly of PyOpenGL?) 
> applied to our servers. However, Chimera is distributed with its own 
> python executable and libraries, so I'm unsure how this type of change 
> could have affected it. I am using the nightly headless linux build of 
> Chimera from 05-13-2014. I have reinstalled chimera from the original 
> .bin file, and I have also installed the most recent nightly headless 
> build. Neither resolved the issue. I'm additionally confused because 
> the exception is raised by tkgui.py, which by naming convention seems 
> like it shouldn't even be called given that I am passing the "--nogui 
> --silent --script" parameters to chimera.
>
> The specific call to chimera is this:
>
> chimera --nogui --silent --script 'lib/PDBMapVisualize.py 1hho 1 maf 
> temp/61098856282.TEMP 1.000000 0.000000 
> data/rcsb/biounit/coordinates/all/1hho.pdb1.gz 
> results/pdbmap_1kg_1hho_20140725-11 -'
>
> Where lib/PDBMapVisualize.py is my script and everything following are 
> arguments to that script. Nothing about this call or the script it is 
> calling have changed between when chimera ran successfully and now.
>
> Any help or advice in resolving this issue would be greatly 
> appreciated. Thanks!
>
> Mike Sivley
> PhD Student in Biomedical Informatics
> Center for Human Genetics Research
> Vanderbilt University Medical Center
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