[Chimera-users] Fwd: Re: Slow dealing with pdb files

Francesco Pietra 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:
> 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 at 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

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