Hi Francesco, The daily builds from the last couple of weeks include an EnsembleCluster tool (under Tools... MD/Ensemble analysis) that you can use for trajectories in a single PDB file. If you had a different format, how to convert to single PDB is described here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-December/ 002142.html I would recommend using ptraj or some similar program to sample your trajectory at time intervals rather than using every single step, if you haven't done that already. Structures from very close time steps are highly correlated with each other and just increase your file size without increasing your information content. Also, as Eric mentioned, you could strip waters or lipid molecules if they are not involved in your analyses. Chimera daily builds can be downloaded here: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Documentation for EnsembleCluster (hasn't made it yet to the "official" web site): http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/ ensemblecluster/ensemblecluster.html This tool clusters the structures and identifies cluster representatives. My opinion is that these are much more meaningful than an "average structure" from a trajectory. 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 On Jan 3, 2008, at 7:18 AM, Francesco Pietra wrote:
Must add that alternatively to "average structure" I tried a cluster analysis with MMTSB. The program refused to work on my trajectories for unclear reasons: the program is installed correctly and the input is correct (as verified by the program author). Therefore, I am eagerly waiting for Chimera being able to carry out cluster analysis (if I understood correctly your message to this regards) francesco