[Chimera-users] Protein RMSD

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 3 13:12:19 PDT 2007

Hi John,
Yes, several.  Let me count the ways...
(I should mention that for those "can Chimera do X?" questions it is  
pretty easy to try Help... Search Documentation in the Chimera menu,  
but you are still welcome to ask)

- the command "match" fits the specified atoms and reports RMSD

- the command "rmsd" reports the RMSD of the specified atoms without  
performing any fitting (simply uses the current positions)

Both of the above require you to specify the exact atoms you want to  
use.  This requires figuring out the correspondences yourself (i.e.  
residue N in one structure should be matching residue M in the other)  
and learning the specification syntax, which is probably the lesser  
difficulty since there are lots of examples in the documentation.

- the tool MatchMaker (under Tools... Structure Comparison) figures  
out for you the N-M residue correspondences by first performing a  
sequence alignment and then matching the aligned residues.  It only  
uses the CA atoms, however.  Also, by default it will iterate the fit  
to exclude CA pairs that are far apart, so what you would get at the  
end is just the "core" result.  You can turn off the iteration to use  
all the aligned residue pairs, and there are also lots of parameters  
you can adjust to control how the initial sequence alignment is  
generated.  The defaults work well in most cases, but I just wanted  
to let you know you can control just about everything.  This tool is  
also implemented as the command "matchmaker".


All of these options report results in the Reply Log (under Favorites).
I hope this helps,
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

On Oct 3, 2007, at 12:01 PM, Beale, John wrote:

> Is there any feature in Chimera that will allow the calculation of  
> the RMSD between a protein and a reference structure?
> Thanks!
> John Beale

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