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

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 3 09:38:32 PST 2008

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:

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:

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

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