Thanks you for the detailed answer! On 10 May 2012 20:39, Greg Couch <gregc@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