Hi John and everybody, I forgot to mention the following additional ways to calculate RMSD in Chimera if you are working with a conformational ensemble (different conformations/configurations of the same set of atoms): - if the ensemble is opened as a trajectory in MD Movie, you can calculate an all-by-all RMSD map http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html (go to the "RMSD Analysis" section) ... also covered in a tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2 - if the ensemble is present as multiple MODELs within a single PDB file opened the normal way in Chimera, you could use the EnsembleMatch tool http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ ensemblematch/ensemblematch.html ... also covered in a tutorial http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembletut.html I don't know if these pertain to the original question, but I mention them for completeness. Best, 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