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 chimera-users)! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu