[chimera-dev] need some scripts from chimera source code

[Eric Pettersen]

On Jun 19, 2009, at 6:04 PM, ylei at ecs.umass.edu wrote:

> 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.html

> Could 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
                         http://www.cgl.ucsf.edu


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