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