Elaine: Please see below. Thans francesco --- Elaine Meng <meng@cgl.ucsf.edu> wrote:
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
My browser tells that this html does not exist, and I was unable to catch it from the last December list. At any event, what I can have (or I am able to get) from ptraj is a series of pdb files for each step. Is the pipermail mentioned above able to combine the pdb files into a single pdb file?
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.
For the case in point, during MD the coordinates were written every 1000 steps, so that I do not restrict ptraj further to this concern.
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
____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs