[Chimera-users] Match -> Align used with a pair of homodimers

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 23 17:51:22 PST 2009

Hi Eric,
A couple of us independently tried the process and did not encounter  
the problem.  Using default matchmaker and match->align parameters,  
the two alignments from match->align had 23% and 21% ID.  However, I  
had a theory of where you might have gone astray.  Here are the steps  
of the process:

(1) generate 1nox dimer as a single model.  Note this is much easier  
in newer versions of Chimera (1.3+):  after creating the dimer using  
BIOMT, you can then use the "combine" command or the "copy/combine"  
action in the Model Panel to merge the two monomer models into one  
dimer model with chains A and B.  No hand-editing!

(2) have 1nox dimer and 1ds7 open in Chimera, use Matchmaker with  
default settings.  This gives a sequence alignment of 1ds7 chain B  
and 1nox-dimer chain A with ~26% ID, as you said, and a pretty good- 
looking superposition: final iteration 101 atom pairs, 1.026  
angstroms RMSD.

(3) in Match->Align, you would choose 1ds7 chain B and 1nox-dimer  
chain A as one pair, Apply to get sequence alignment with 23% ID  
(default parameters in Match->Align).  Choosing 1ds7 chain A and 1nox- 
dimer chain B as another pair, clicking Apply gives another sequence  
alignment with 21% ID.

My theory is that maybe you chose A and A as one pair, B and B as  
another pair whereas the superposition really has each A chain on top  
of a B chain.

I hope this helps,
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

On Feb 23, 2009, at 4:41 PM, E. Merkley wrote:

> Hello chimera friends:
> I am trying to get a structure-based sequence alignment for a pair of
> homologous proteins that are homodimers.  If I proceed as described  
> in the
> tutorial and in the 2006 BMC Bioinformatics paper, by first using
> Matchmaker, then using Match -> align, the Match -> Align fails to  
> produce
> a reasonable alignment.  The sequence identity from the Matchmaker  
> output
> is 26.5%, but only 1.0 % from the Match -> Align step. If I delete the
> second monomer from each protein, Match -> Align works quite well.
> However, it seems like this alignment won't take into account any
> differences in the tertiary structure between the two proteins.   
> That is,
> I think I want the global alignment of the whole dimer for the  
> structural
> alignment, since the active sites is are at the interface.  Any
> suggestions?  I'm using version 1.2540, and my two proteins are PDB  
> codes
> 1ds7 and 1nox (1nox dimer built from BIOMT matrix in Chimera and
> hand-edited to be 1 model with A and B chains).
> Thanks yet again,
> Eric

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