[Chimera-users] rmsd cluster analysis

Francesco Pietra chiendarret at yahoo.com
Tue Dec 18 09:46:03 PST 2007

I had carried out successfully all-by-all pairwise RMSD. Though, it does not
help much comparing different ligands for the same protein. As to MMTSB, there
are indications about the compilation that I do not understand yet. All in all,
it seems to me that a tool for performing affinity analysis for ligands in
explicit medium (ideally free energies) is not easily at hand.

Hope I am wrong and someone comes with suggestions (I posted the problem of
affinities in explicit medium yesterday to DOCK, so a suggestion might come
from there too).


--- Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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

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