[Chimera-users] rmsd cluster analysis

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 18 09:31:15 PST 2007

Hi Francesco,
The MD Movie tool (which replays trajectories) can also calculate all- 
by-all pairwise RMSD values and show them as a grayscale map.  In the  
map you can see which frames are similar to which, but the tool does  
not really perform clustering.

MD Movie (see "RMSD Analysis" section):

The "Trajectory and Ensemble Analysis" tutorial (part 2) uses this  
tool and shows an example RMSD map:

Perhaps the AMBER tutorials would be more useful in your situation.   
I believe tutorial B3 includes clustering:

I hope this helps,
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

On Dec 18, 2007, at 6:25 AM, Francesco Pietra wrote:

> Is it feasible to command a cluster analysis from rmsd? I would  
> like to group
> for likeliness snapshots from MD with respect to, say, the  
> structure from which
> MD was started.
> Thanks
> francesco pietra

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