Hi Francesco and others, People with MD trajectories can also use this new EnsembleCluster tool (available in the most recent daily builds) by: - viewing the whole trajectory with the "MD Movie" tool, or at least all the frames you want to cluster - from the MD Movie dialog menu, choosing File... Save PDB and saving "all frames" to a file - quitting from MD Movie and opening the new file with File... Open - choosing Tools... MD/Ensemble Analysis... EnsembleCluster, clicking the line that shows that new file, then OK I just tried this to make sure it works. The clustering calculation may take a while, but eventually another dialog with results should appear. This tool is still under development and may change, but this will at least allow users to try it on trajectory ensembles as well as NMR ensembles. 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