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@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