Hi Ben, I can answer parts of the question. The clustering is a reimplementation of what is described in 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. <http://www.ncbi.nlm.nih.gov/pubmed/8961360> This reference is given in the Ensemble Cluster docs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html> (and the MD Movie clustering docs link to this page; from MD Movie tool, click Help button and go to the clustering section of the resulting page) Clustering is not available as a Chimera command. Chimera capabilities can be accessed with python scripts, but I will have to leave any details on that, as well as how to save results (other than saving your Chimera session), for the others to provide. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 2, 2012, at 7:46 AM, Benjamin SCHWARZ wrote:
Hi list,
I clustered a bunch of structures using the MD clustering tool, I am very happy with the result but I can't find how to download/save the result.
Is there a way for instance to copy-paste the columns indicating the number of models as well as the index of the representative for each cluster; alternatively, is possible to sort out frames by clusters ?
If there are command shortcuts to manipulate the clustering, I'd be happy to get them, or to get a link to it in the manual. Chimera is really a great tool, but the learning curve appears really steep ;)
Ultimately, I wonder about the type of clustering used here. I suspect a complete linkage but I couldn't find the confirmation in the manual. Any info on that ?
Thanks a lot for your extremely good work, and the fast answers on this mailing list
--Ben