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 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++