[Chimera-users] Automated RMSD Calculations

[Elaine Meng]

Hi Nancy,
This email list is mainly intended for Chimera questions.

In Chimera, you could take a look at the commands "match" (which will superimpose to get least-square-fit RMSD) and "rmsd" (which will simply use the input coordinates):

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

However, you would have to take care of the "automation" part by writing a script containing the appropriate commands.  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 Mar 25, 2011, at 3:11 PM, Nancy wrote:

> Hi All,
> I would like to calculate RMSDs of a large number of small molecule conformations against a reference conformation, is there a simple software program or method that can be used to perform such calculations?
> Thanks in advance,
> Nancy