[Chimera-users] rmsd

[Elaine Meng]

Dear Simone,
Yes, there are many possible ways to calculate protein-protein RMSD in Chimera.

If you want Chimera to figure out the fit and superimpose the proteins for you, try MatchMaker: this uses the sequences and helix/strand locations to figure out how to superimpose the proteins, then reports RMSD and how many alpha-carbon pairs were used to calculate the RMSD.  MatchMaker is in the menu under "Tools... Structure Comparison."   It has several options.  The RMSD would be given in the Reply Log (in menu under "Favorites").

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> 

If you want to tell Chimera specific residue numbers and atoms to fit, instead use the "match" command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>

Or, if you do not want to superimpose, only calculate the RMSD in the current non-fitted positions, the "rmsd" command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

Or, if you have a molecular dynamics trajectory or NMR ensemble of many copies of the same structure, there are additional methods for calculating all-by-all RMSD values.  

Discussion of all these methods and links to more details:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.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

On Nov 8, 2011, at 2:08 AM, sdimicco wrote:

> Dear Chimera developers, 
> is it possible to calculate the rmsd between two proteins by the softwere? How can I do it? 
> Thank you in advance.
> Simone