Hi all,
I am comparing 4 very similar (<1.5A rmsd) large (750 residues) structures,
but struggling to find a way to generate a figure that conveys where they
are most alike and where they diverge.
Simply drawing a superimposed set of backbone traces results in what looks
like colored spaghetti. I don't think that's going to work.
So I had the idea of drawing a single backbone trace, or ribbon diagram,
and coloring by the RMSD of the four C-alphas at each residue position.
But I can't find a program that will output this as a table of numbers
I can use. All of the multiple structure superposition programs must
have this information internally. After all, that's what they are minimizing.
But do any of the programs provide an option to write it out?
I can get pairwise per-residue deviations by doing SSM superposition in Coot,
but that doesn't get me to an RMSD for all four structures jointly.
Ethan
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Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
