[Chimera-users] nmrclust: linux terminal
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:
> 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?
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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