[Chimera-users] MD analysis : get clusters

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 2 09:09:33 PDT 2012


Hi Ben,
I can answer parts of the question. The clustering is a reimplementation of what is described in this paper:
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Kelley LA, Gardner SP, Sutcliffe MJ. Protein Eng. 1996 Nov;9(11):1063-5.
<http://www.ncbi.nlm.nih.gov/pubmed/8961360>

This reference is given in the Ensemble Cluster docs:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html>
(and the MD Movie clustering docs link to this page; from MD Movie tool, click Help button and go to the clustering section of the resulting page)

Clustering is not available as a Chimera command.

Chimera capabilities can be accessed with python scripts, but I will have to leave any details on that, as well as how to save results (other than saving your Chimera session), for the others to provide.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 2, 2012, at 7:46 AM, Benjamin SCHWARZ wrote:

> Hi list,
> 
>   I clustered a bunch of structures using the MD clustering tool, I am very happy with the result but I can't find how to download/save the result. 
> 
> Is there a way for instance to copy-paste the columns indicating the number of models as well as the index of the representative for each cluster; alternatively, is possible to sort out frames by clusters ?
> 
> If there are command shortcuts to manipulate the clustering, I'd be happy to get them, or to get a link to it in the manual. Chimera is really a great tool, but the learning curve appears really steep ;)
> 
> Ultimately, I wonder about the type of clustering used here. I suspect a complete linkage but I couldn't find the confirmation in the manual. Any info on that ?
> 
>    Thanks a lot for your extremely good work, and the fast answers on this mailing list
> 
>      --Ben
> 




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