[Chimera-users] matchmaker output
meng at cgl.ucsf.edu
Wed Mar 4 09:37:29 PST 2009
> I want to simplify the question I asked yesterday. Is there any way to
> store the output of Match Maker, specifically the RMSD values for
> residue and the list of residues in the alignment regions in an
> external file from command line?
I just wanted to bring up a related issue: the sequence alignment you
get from MatchMaker is not a fully structure-based alignment. If the
sequences are fairly easy to align, this is not an issue, but when
sequence identity is low, you may want to generate a structure-based
sequence alignment with Match->Align after superimposing the
structures with MatchMaker.
More explanation... by default, MatchMaker:
(1) generates a pairwise sequence alignment using standard methods.
Some structure information is used at this step because the alignment
score includes both residue type (alanine, arginine, ...) and
secondary structure (helix, strand ...).
(2) uses the sequence alignment to fit the structures. At first all
columns are used, but iterating the fit discards the columns where the
structures match poorly in space. If there are sections of the
alignment that are wrong, the iteration process tends to exclude them
from fitting, resulting in a good-looking superposition. Therefore,
a successful and correct superposition (as determined by eye) does not
mean all the parts of the sequence alignment are right.
If the sequences are similar enough that you don't think errors in the
MatchMaker sequence alignment are an issue, saving the residue pairing
and RMSD header (which for pairwise is simply the CA-CA distance)
directly from that alignment is fine. If you are getting into the
twilight zone of sequence similarity, I suggest running Match->Align
on the superposition, then proceeding with that second sequence
alignment instead. Another advantage of Match->Align is that it can
make a single sequence alignment of >2 superimposed structures.
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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