[Chimera-users] clustering of docking results

[Elaine Meng]

Hi Bala,
We don't have any tools specifically for clustering docking results.  We do have a general clustering tool that works on ensembles (identical atoms, so would not work if your docking results are different molecules).  This clustering does not use any reference structure or docking scores.  It is the Ensemble Cluster tool:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html>

If your docking results were all the same molecule, just different positions/conformations all in one PDB or Mol2 file, you try using File... Open or the open command to open it, then use this tool for clustering (under Tools... MD/Ensemble Analysis).  I don't know if it would do the type of clustering you had in mind, however.  You may have to use some other program for that.
Best,
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 29, 2010, at 3:09 AM, Bala subramanian wrote:

> Friends,
> I am using viewdock tool for analysing the docking result obtained from autodock. Is there any way to do some clustering of the docked conformations using the energetically best structure as the reference within chimera ?
> Thanks in advance,
> Bala