[Chimera-users] Match -> Align used with a pair of homodimers
E. Merkley
edm4 at u.washington.edu
Mon Feb 23 16:41:59 PST 2009
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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