You cannot easily start Python and import Chimera. There are a few reasons for this. 1) An environment variable needs to be set (LD_LIBRARY_PATH) so Chimera libraries can be found, 2) an environment variable (PYTHONPATH) needs to be set so Python can find Chimera modules, 3) Chimera requires exactly the Python binary that comes with it so that the dozens of compiled modules work correctly and unicode handling is done as expected. Because of the difficulties we don't support importing Chimera in an already running Python -- but with work you could figure it out. The Chimera programming documentation describes how to get surface geometry from a surface model: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/surface.html To calculate the surface in the first place you need to look at the Python code I mentioned. Unfortunately, most Python routines Chimera provides are not documented, so you will have to read the code that comes with the Chimera distribution in the "share" directory. Another aid is to look at the Chimera Python scripts web page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom
Thank you! So I can't just open a new python script and import chimera without ./chimera
I still don't know how to get the surface data(It's all triangles right?) say:
import chimera mlist = chimera.openModels.list() molecule = mlist[0] Then what should I do to get the surface calculated and get the data?
Forgot to mention the mscalc Python interface is the Python MolecularSurface module found in
chimera/share/MoleculeSurface
or on the Mac in
Chimera.app/Contents/Resources/share/MoleculeSurface
Look at the calcsurf.py code which runs the mscalc stand-alone program
(include in Chimera) and look at msurf.py if you are interested in the
Chimera SurfaceModel class which displays the surface in the graphics
window.
Tom
Hi chimera users, I'm wondering about several question: I installed chimera in my home dir, what's path to import in python? how can I access the data generated by mscalc in python?