[Chimera-users] matchmaker output

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 3 16:26:29 PST 2009

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?

Hi Karan,
	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.
	Let me know if you have questions.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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