[Chimera-users] clustering

Rafael Rocha rafael.eduardo.oliveira.rocha at gmail.com
Fri May 22 06:48:01 PDT 2015

Thank you Elaine , his answer was very illuminating .

2015-05-21 14:39 GMT-03:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html
> >
>  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.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblematch/ensemblematch.html
> >
> 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
> ----------
> 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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