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