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

Sierk, Michael michael.sierk at email.stvincent.edu
Wed Jul 20 09:43:52 PDT 2011

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?

Mike Sierk

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
"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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