[Chimera-users] Cutoff for clustering

[Elaine Meng]

Hi Yasser,
It does not use a specific RMSD value that fits all cases, but instead determines the cutoffs from the data.  The method is described in the paper cited near the top of the Ensemble Cluster manpage:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html>

Namely, 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.
<https://pubmed.ncbi.nlm.nih.gov/8961360/>

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

> On Feb 15, 2021, at 8:09 AM, Yasser Almeida <yasser.almeida at gmail.com> wrote:
> 
> Hello,
> 
> I have a question regarding the clustering in the MD Movie tool (MD Movie/Analysis/Cluster). What's the RMSD cutoff value to make the clustering? I don't see any mention of this in the documentation.
> 
> Thanks in advance,
> -Yasser