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

[Sierk, Michael]

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?

Thanks,
Mike Sierk

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Michael Sierk                                                      Email: michael.sierk<AT>email<dot>stvincent<dot>edu
Assistant Professor of Bioinformatics                  Phone: (724) 805-2367
Saint Vincent College                                         Office: Physics 205
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"There is something fascinating about science. One gets such wholesome
returns of conjecture out of such a trifling investment of fact." -- Mark Twain.
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