Hi all
I am working on a project that requiring some program scripts concerning with
1) Compute Amber Energy Function
2) Read rotamer information from the Dunbrack Backbone-dependent
Rotamer library
3) Read in Electron Density Map and get the density value for each 3-D
point in the crystal
I did check some related python files in the source code folder and
can understand them to some extent, but for running these files, some
modules (e.g. Chimera, Rotamers) are needed. However, I don't know how
to install these modules, or maybe I should recompile Chimera from
source code first(If so, then how, because I don't know the procedure
either. BTW, my platform is mac osx)?
Well, Chimera is itself a Python interpreter. So if you open a Python script (ending in .py) with either File->Open or with the "open" command then Chimera will run that script. The script can import any of the modules provided by Chimera (e.g. "import chimera" or "import Rotamers"). If you need to run a script without Chimera's interface coming up or need to provide arguments to your script, see the "--nogui" and "--script" arguments (respectively) documented here:
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.htmlCould someone show me which files I should use for the above mentioned
three subjects and what kinds of modules I should install and how?
For (1), we would need more details. What are you trying to do? Compute charges? Minimize structures?
For (2) you would use the Rotamers module, probably either the getRotamers function or the useBestRotamers function, depending on your needs.
For (3) I think we would need a better description of what you are trying to accomplish, but you can certainly open a density map with:
from chimera import openModels
density = openModels.open("map_file_name_with_proper_suffix")[0]
I'm not an expert on how to get the density value at a point, but maybe Tom Goddard from our lab (who wrote the volumetric data code) will chime in on how to do that.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab