[Chimera-users] rmsd cluster analysis

[Elaine Meng]

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):
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ 
framemovie.html

The "Trajectory and Ensemble Analysis" tutorial (part 2) uses this  
tool and shows an example RMSD map:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
ensembles2.html#part2

Perhaps the AMBER tutorials would be more useful in your situation.   
I believe tutorial B3 includes clustering:
http://amber.scripps.edu/tutorials/

I hope this helps,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html

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