[Chimera-users] rmsd cluster analysis

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 20 15:58:31 PST 2007

Hi Francesco and others,
People with MD trajectories can also use this new EnsembleCluster  
tool (available in the most recent daily builds) by:

- viewing the whole trajectory with the "MD Movie" tool, or at least  
all the frames you want to cluster
- from the MD Movie dialog menu, choosing File... Save PDB and saving  
"all frames" to a file
- quitting from MD Movie and opening the new file with File... Open
- choosing Tools... MD/Ensemble Analysis... EnsembleCluster, clicking  
the line that shows that new file, then OK

I just tried this to make sure it works.  The clustering calculation  
may take a while, but eventually another dialog with results should  
appear.  This tool is still under development and may change, but  
this will at least allow users to try it on trajectory ensembles as  
well as NMR ensembles.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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