[Chimera-users] Ensemble cluster

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 19 10:04:49 PDT 2013

Hi Damien,
The clustering is based on pairwise best-fit RMSDs, without moving the structures.  In other words, the spatial locations and orientations of the structures are not important, only their conformations.  So you may see spatially separated "clusters," but the clustering obtained based on pairwise conformational comparisons may be completely different.

Ensemble Cluster documentation:

Although RMSD-without-fitting values can be calculated with the "rmsd" command, I don't know of any automatic way to use that for clustering in Chimera.

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

On Jun 19, 2013, at 7:12 AM, Damien Larivière wrote:

> Dear All,
> As a preamble, it is quite possible that I completely misunderstood the way to use the Ensemble cluster tool.
> Here is the problem I face:
> I opened a PDB file containing 8 models. The models have the same number of atoms, the same numbering, the format is Model Endmdl, etc. 
> I launched Ensemble cluster in order to identify clusters. From the image below, one can see visually 2 clusters. Chimera effectively identifies 2 clusters but the representatives of each (in red and blue-turquoise) belongs to the same cluster. I expected one representative in each of the two clusters.
> May you tell me what is wrong with my understanding?
> Many thanks for your help,
> Damien
> ps : Is there a way to cluster according to a previously chosen RMSD?

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