[Chimera-users] clustering

Elaine Meng meng at cgl.ucsf.edu
Thu May 21 10:39:48 PDT 2015

Hello Rafael,
Normally this tool is only used for ensembles where each structure contains exactly the same atoms (such as from NMR structure determination, or snapshots from MD trajectories).

In your case, it might be possible to try it with structures that have different atoms, but I don’t know how well it would work.  Also, the atoms you want to use would still need to have exactly the same names in each structure.  If so, then to try using Ensemble Cluster you would have to:

(1) put all the structures in a single PDB file, with MODEL/ENDMDL lines separating them.  You can have Chimera create this file by opening all your structures from separate files, then choosing menu: File…Write PDB, then in the resulting dialog choosing all of the structures in the “Save models” section and “Save multiple models in: a single file”.  Then close all the original models and open your new single file.

(2) start Ensemble Cluster, specify the set of atoms (again, must have same names in each structure, and also same residue number, if there are other residues you don’t want to use that also have those atom names).

For your second question, sorry, you cannot change the RMSD cutoff in Ensemble Cluster because the method figures it out automatically based on the data.  For more details on the method, see citation in:

 If you don’t have that many ligands, you could try using the Ensemble Match tool instead, specifying the single file (see #1 above) as both reference and alternative.  Again this requires specifying atoms that have the same specification (atom names and possibly residue names, if needed) in each structure.  It will display an N X N grid of the resulting RMSD values.

However, you may need to find another program for this purpose.  It may be that Chimera is not effective for what you want to do.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 20, 2015, at 7:22 AM, Rafael Rocha <rafael.eduardo.oliveira.rocha at gmail.com> wrote:
> hello,
> I have a set of ligands that share Some atoms in common. How I can clustering only those atoms?
> Also, how I can change the variation of RMSD for this cluster analysis  in the "ensemble cluster" tool of chimera?
> Thanks,
> Rafael.

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