[Chimera-users] Using Chimera from non-chimera python scripts

Greg Couch gregc at cgl.ucsf.edu
Thu May 10 10:39:59 PDT 2012

While it is possible to use chimera's python packages and modules 
outside of chimera, it is messy.  It is *much* easier running the python 
script using chimera.  If you have a third party package that you want 
to use with chimera, you can install it into chimera's python using:

      chimera --nogui --silent --script "setup.py install"

instead of:

      python setup.py install

It is also possible to make easy_install work with chimera by 
temporarily putting chimera's bin directory on your path and running the 
appropriate egg (see http://pypi.python.org/pypi/setuptools for 
details). Right now, chimera is using Python 2.7.

To create images in nogui mode, you need to use the experimental 
headless version of chimera that runs on Linux.  We consider it 
experimental because some of chimera's older functionality doesn't work 
yet in nogui mode.  If you come across a nogui limitation in your work, 
please file a bug to increase its priority to be fixed.

An alternative to nogui mode would be to run chimera with a virtual 
framebuffer, that could be because chimera is running on a virtual 
machine (e.g., vmware), or, on Linux using Xvfb.  The advantage of the 
virtual machine is that you can run any version of chimera you're 
comfortable with.



On 05/10/2012 06:02 AM, Dan Cohen wrote:
> Hello,
> I would like to use Chimera python classes from a python script 
> running outside Chimera (part of a larger python project).
> I saw another post that explained that this could be done but I was 
> unclear which of the Chimera functionality can be used
> in this case. In case I want to create an image (e.g. load pdb files, 
> do some editing and then create an image to a file) - can I use
> the "chimera" class or do I need to use something else? (I saw a 
> reference to "midas" classes)
> Is there an example for doing that? Processing a file and creating an 
> image in a non-GUI scenario running outside chimera?
> Thank you,
> Dany

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