[Chimera-users] superimposing active sites

[Elaine Meng]

On Jul 23, 2008, at 6:18 PM, Maria wrote:

> Elaine,
> I have created active sites by using the zone in
> chimera for 72 proteins.  Is there a way I can
> do structural superimposition of the active
> sites using chimera?
> Thanks,
> Maria


Hi Maria,
Sure, there are many, many ways to superimpose structures in Chimera.

If the structures are homologous (have the same fold, usually also  
some sequence similarity), probably the easiest are these two methods:

(A) MatchMaker tool (or the "matchmaker" command, which acts exactly  
the same way) - it creates a sequence alignment and then uses those  
alignment columns to superimpose the structures

(B) if you already have a sequence alignment, you can open that in  
Chimera and use it to superimpose the structures

With both (A) and (B) you would use the whole structures - it is OK if  
you are only displaying a zone as long as the other atoms are still  
there (are merely hidden, not deleted).

Some other approaches can be used for either homologous or  
nonhomologous proteins:

(C) "match" command - you specifically name the atoms you want to use  
for fitting in the command; for example, atoms from a few active site  
residues and/or from the ligand

(D) interactive fitting "by hand"

Links to more detailed information...

Discussion and examples of more than one method:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#superimposing
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#comparison
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#matching

MatchMaker man page:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html

"matchmaker" command man page:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html

"match" command man page:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html

Using a pre-existing sequence alignment:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html
(see "Structural Superposition" section)

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html