[Chimera-users] Ensemble cluster

Damien Larivière damien.lariviere at fourmentinguilbert.org
Wed Jun 19 07:12:49 PDT 2013

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,


ps : Is there a way to cluster according to a previously chosen RMSD?

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