[Chimera-users] Assisstance to claculate RMSD value

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 7 09:58:34 PDT 2016


Dear Shreyas Iyer,

You can compare related protein structures by superimposing them with MatchMaker (in menu under Tools… Structure Comparison) or its command version “matchmaker”.  This will give the RMSD in the Reply Log (menu: Favorites.. Reply Log).

Description and instructions, graphical interface:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>

…command, including examples:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>

Matchmaker uses only one atom per residue, the alpha-carbons (CA atoms). If you want to use more atoms or different atoms you would have to use the “match” command instead.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>

I hope this helps,
Elaine
-----
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. The email address for Chimera questions is chimera-users at cgl.ucsf.edu (as CC’d here).

On Oct 7, 2016, at 4:09 AM, Shreyas Iyer <shreyas.i.imsc14 at ahduni.edu.in> wrote:

> Respected Sir/Madam,
> 
> I wanted to know how to calculate RMSD values between any 2 homology models of a protein with the help of USCF Chimera. Please guide me as soon as possible.
> 
> Awaiting a positive reply.
> 
> Yours Sincerely,
> Shreyas Iyer




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