On Mar 2, 2009, at 1:47 PM, Karan Uppal wrote:

Hello,

I am trying to write a Python script to extract the header information
from the MultAlign Viewer tool. Are there any command-line commands to
interface with this tool and save the header information without
manually using the toolbar.

On Mar 3, 2009, at 9:49 AM, Karan Uppal wrote:

Hello,

I want to simplify the question I asked yesterday. Is there any way to
store the output of Match Maker, specifically the RMSD values for every
residue and the list of residues in the alignment regions in an
external file from command line?

There is an underlying function in MatchMaker (MatchMaker.match) that can be called from Python to perform the same work as MatchMaker and retrieve the matching information. I've attached a script that uses the function to match chain A of two open models (the script assumes exactly two structures are open) and print the RMSD, residue pairs, and their CA-CA distances to the reply log. You should look over the script and the definition of the match function (in chimera/share/MatchMaker/__init__.py) and modify it to suit your needs. I assume you know enough Python to convert the plain print statements into the equivalents needed to output to a file.