[Chimera-users] Command line

Eric Pettersen pett at cgl.ucsf.edu
Thu Apr 21 14:03:41 PDT 2011

On Apr 21, 2011, at 11:15 AM, Elaine Meng wrote:

> (B) text file with summary info.  We don't have commands for that.   
> For things that are Chimera attributes, for example areaSAS for  
> residues, you would open Render by Attribute (under Tools...  
> Depiction or Structure Analysis), show the desired attribute in the  
> histogram, and then use that tool's File menu to save the attribute  
> values to a file.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html 
> >
> The number of ions, ligands, chains aren't attributes as far as I  
> know.  You would have to do something yourself such as "select  
> ligand" and then see how many residues were selected.

If you really need to script behavior like (B), you'll have to resort  
to Chimera's Python-language interface rather than its command- 
language interface.  So if you really need to go that route it would  
behoove you to familiarize yourself with the Python language (www.python.org 
), look through the Chimera programmer's documentation (www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html) 
, and then start asking questions (possibly on chimera-dev instead of  


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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