Are you using the latest daily build of Chimera? About two or three weeks ago, I made some changes that decreased run time by quite a bit. If you are using the latest, can you please send me your data file so I can try to track this down. Also, if you are clustering proteins, you might try to specify "@CA" in the "Parts to Match" field of the Ensemble Cluster panel. A lot of time is spent in pairwise alignment of structures to compute the RMSD; so the fewer atoms it needs to match, the fast the algorithm. Regarding a script, what information do you want to retrieve from the clustering results? The clusters, the representative for clusters, the pairwise RMSDs, etc? Conrad Austin B. Yongye wrote:

Hi everyone, I am trying to use nmrclust to cluster a set of about 5K conformers with the chimera gui. It is been ~5hrs now, and still running. I was wondering whether the algorithm can be run via the linux terminal. I found this posting:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003195.html

Could some one please let me know how to use this python code to run the clustering in the linux terminal invoking the python environment?

Thanks, Austin-

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