[Chimera-users] nmrclust: linux terminal

Conrad Huang conrad at cgl.ucsf.edu
Thu Nov 12 08:59:22 PST 2009

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?


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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