[MMTK] Comparing normal modes for different proteins

Ramon Crehuet rcrehuet at gmail.com
Sun Mar 18 20:32:45 UTC 2007


Hi all,
   I'd like to compare the normal modes of a set of proteins which are
quite similar (in RMS and sequence identity). I know this can be
tricky because it involves comparing things of different universes (I
can't see a way of putting all the proteins in the same universe).
   I need to compare residue-by-residue so that, for a given mode, I'd
like to know to which residue and which atom does mode[i] refer to. I
know the usual way to do things is the opposite, letting MMTK do the
transformation as in positions = universe.configuration().
So, in a nutshell, I want to project the modes of one pdb onto the
modes of another, choosing which residue projects onto which one
(there might me deletions in one sequence, etc). I had in mind using
Biopython for parsing the sequence alignment, but that is another
issue.
   Maybe there is a completely different way to set the problem. Any
idea is welcome.
Thanks in advance,
Ramon



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