[Chimera-users] Structure -> Match in a script

[Eric Pettersen]

On Jul 20, 2011, at 9:43 AM, Sierk, Michael wrote:

> All -
>
> I would like to write a command file that will automatically read in  
> two structures and a corresponding alignment file, then perform the  
> superposition (and coloring, etc.).  I can read in the pdb and pir  
> files using the command line, and I can do the superposition in the  
> Multalign Viewer using Structure->Match, but I cannot figure out how  
> to do the superposition based on the sequence using the command  
> line.  I think if there was a way to select the residues that are  
> aligned in the sequence alignment I could use the "match" command,  
> but I don't see a way to do that.  Is there an attribute analogous  
> to mavPercentConserved that corresponds to "aligned"?  Or is there  
> an automatically generated region based on the sequence alignment?

There are no command equivalents to Multalign Viewer menu items  
unfortunately.  However, using a Python script you can cheat your way  
around that by locating the Multalign Viewer Python object and  
invoking its match method.  I've attached a script that will invoke  
match on the newest Multalign Viewer instance open in Chimera.  If you  
want to employ iteration in the matching, change this line of the  
script:

mav.match(associatedStructures[0], associatedStructures[1:])

to:

mav.match(associatedStructures[0], associatedStructures[1:],  
iterate=True, iterateCutoff=2.0)

You can execute the Python script in the middle of your Chimera script  
by simply using the "open" command to open it, e.g. "open ~/mavMatch.py"

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

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