Hi Francesco, The MD Movie tool (which replays trajectories) can also calculate all- by-all pairwise RMSD values and show them as a grayscale map. In the map you can see which frames are similar to which, but the tool does not really perform clustering. MD Movie (see "RMSD Analysis" section): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html The "Trajectory and Ensemble Analysis" tutorial (part 2) uses this tool and shows an example RMSD map: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2 Perhaps the AMBER tutorials would be more useful in your situation. I believe tutorial B3 includes clustering: http://amber.scripps.edu/tutorials/ 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 Dec 18, 2007, at 6:25 AM, Francesco Pietra wrote:
Is it feasible to command a cluster analysis from rmsd? I would like to group for likeliness snapshots from MD with respect to, say, the structure from which MD was started. Thanks francesco pietra