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

[E. Merkley]

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