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

Dan Cohen bojemoi at gmail.com
Fri May 11 10:03:15 PDT 2012

Thanks you for the detailed answer!

On 10 May 2012 20:39, Greg Couch <gregc at cgl.ucsf.edu> wrote:

> 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<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.
>    HTH,
>    Greg
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120511/b8892252/attachment.html>

More information about the Chimera-users mailing list