[Chimera-users] matchmaker output

Elaine Meng 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  
> every
> 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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