Hi Thomas, While the trajectory RMSD analysis and Ensemble Match are for ensembles (same set of atoms, only coordinates differ), you can certainly calculate RMSDs between different proteins in various ways: (a) match command, with atoms to use specified in the command (b) matchmaker tool or command, where alignment is figured out for you and then a CA-only RMSD is computed (c) using your input sequence alignment, again a CA-only RMSD is computed <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> All of those allow iterating the fit or not as you prefer. However, only (a) and (b) are available as Chimera commands. Method (c) could be done with python (someone else would have to advise you on the details) after you open your sequence alignment. However, maybe the alignment from (b) would be good enough for you -- it generally works well, you can use the "show alignment" option to view and check it. The MD Movie tool allows entering a script to be executed at each frame, and the script can be either Chimera commands (allowing methods a-b above) or Python (method c). See "per-frame scripts" in: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> First work out the necessary command by just trying it in the Command Line on a single frame of the trajectory (or simply opening a python file to execute it). Then once it is satisfactory, enter it as a per-frame script and play the whole trajectory from start to end. The RMSDs would be reported in the Reply Log (you would probably want to clear the log first). 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 May 15, 2012, at 1:52 PM, Thomas Evangelidis wrote:

Dear UCSF Chimera developers,

I want to calculate the RMSD between a MD trajectory of a protein and the crystal structure of its paralogue protein. I have looked though the Ensemble Match and RMSD Analysis pages but these applications work for the same proteins (correct me if I am wrong). Is there any way to provide an alignment file to Chimera and calculate the time series of the RMSD between the two paralogues?

Thanks in advance, Thomas