Hi David,
The clustering description in the MD Movie (trajectory viewer) page says to see Ensemble Cluster for details:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#clustering>

Here is the Ensemble Cluster documentation, including literature reference for the method:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html>

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

> On Jul 10, 2018, at 1:29 PM, David Adrian Saez San Martin <davidsaez@udec.cl> wrote:
>
> Hello, I want to use Chimera to generate clusters of a molecular dynamics trajectory. I have been looking for info about the clustering algorithm it uses, but I was not able to find anything. I guess it employs a default technique, does anybody know which one?
> Regards.
> David-.