[Chimera-users] structural similarity measures in Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 30 21:04:19 PDT 2010

Dear Minming,
Dr. Ferrin forwarded your question to me.

We recently added calculation of structure similarity measures to  
Chimera.  This capability is not in versions 1.4/1.4.1, but only in  
1.5 (recent daily builds, which are also available from our download  
page). In such recent builds, the "Match -> Align" tool (under  
Tools... Structure Comparison in the menu) calculates two measures  
that have been described in previous publications, the SDM and the Q- 
score.  The SDM has been used to construct phylogenetic trees before.   
I don't know if the Q-score has been used that way.

Documentation for Match->Align and details of these measures:

However, there are some issues that may affect whether you decide to  
use Chimera to calculate these values for your structures:

(1) You would need to run Match->Align for each pair.  There is no  
option to do all pairwise comparisons on multiple structures.  You  
would need to script looping through all pairs (with python or shell  

(2) There is no Chimera command for Match->Align.  Thus Match->Align  
would also need to be run via python.  I don't have scripting  
expertise, so someone else would have to provide more details if you  
decide to try this.

(3) Before you run Match->Align, the structures need to be  
superimposed.  We purposefully made Match->Align independent of the  
superposition method.  There are several possible ways to superimpose  
structures in Chimera,
but probably the easiest in your case would be MatchMaker, which is  
also available as a Chimera command (matchmaker or mmaker, see that  
URL and links within).  Usually the mmaker defaults work pretty well,  
for example Chimera commands:

open 2mnr
open 4enl
mmaker #0 #1

(Then you could try running Match->Align interactively.  The SDM, Q- 
score, etc. are reported in the Reply Log, opened with Favorites...  
Reply Log in the menu.)

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. we recommend sending Chimera questions to chimera-users at cgl.ucsf.edu 
   (I CC'd that list here after removing the details from your  
original mail)

> -------- Original Message --------
> Subject: A question about your software(UCSF Chimera)
> Date: Tue, 23 Mar 2010 21:55:06 -0400
> Dear Dr. Ferrin,
> I am very interested in using your software UCSF Chimera, which have  
> some
> commands that can do the job of aligning and measuring a distance
> between two
> protein structures.
> I am a PhD student at Purdue University working on the evolution of  
> protein
> structure with Professor Peter Waddell. I was hoping to use your  
> structure
> alignment software to obtain a pairwise structure distance matrix.  
> This
> matrix
> will then be used in phylogenetic analyses, comparing the trees and
> “treeness”
> of that structural distance compared to that produced by other  
> published
> methods.
> [...]
> Could you please tell me if your structural alignment software can  
> easily
> produce a complete pairwise distance matrix for a list of ~50
> structures? I did
> not see a way to do this. If not, is there any easy way to modify it  
> to
> do this?
> [...]
> Best Regards and Sincerely,
> Minming Li

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