[Chimera-users] Fwd: Re: Slow dealing with pdb files
chiendarret at yahoo.com
Thu Jan 3 13:23:24 PST 2008
Please see below. Thans
--- Elaine Meng <meng at 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:
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:
> Documentation for EnsembleCluster (hasn't made it yet to the
> "official" web site):
> 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.
> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 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.
More information about the Chimera-users