Hi John, Yes, several. Let me count the ways... (I should mention that for those "can Chimera do X?" questions it is pretty easy to try Help... Search Documentation in the Chimera menu, but you are still welcome to ask) - the command "match" fits the specified atoms and reports RMSD http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html - the command "rmsd" reports the RMSD of the specified atoms without performing any fitting (simply uses the current positions) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html Both of the above require you to specify the exact atoms you want to use. This requires figuring out the correspondences yourself (i.e. residue N in one structure should be matching residue M in the other) and learning the specification syntax, which is probably the lesser difficulty since there are lots of examples in the documentation. - the tool MatchMaker (under Tools... Structure Comparison) figures out for you the N-M residue correspondences by first performing a sequence alignment and then matching the aligned residues. It only uses the CA atoms, however. Also, by default it will iterate the fit to exclude CA pairs that are far apart, so what you would get at the end is just the "core" result. You can turn off the iteration to use all the aligned residue pairs, and there are also lots of parameters you can adjust to control how the initial sequence alignment is generated. The defaults work well in most cases, but I just wanted to let you know you can control just about everything. This tool is also implemented as the command "matchmaker". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ matchmaker.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html All of these options report results in the Reply Log (under Favorites). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 3, 2007, at 12:01 PM, Beale, John wrote:

Is there any feature in Chimera that will allow the calculation of the RMSD between a protein and a reference structure?

Thanks! John Beale