[Chimera-users] average vs ensemble

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 29 12:43:34 PST 2008

Hi Rachel,
This may be just a personal opinion (others, feel free to pipe up!),  
but I would go for representatives as opposed to averages.   
Presumably each ensemble member has reasonable internal coordinates,  
whereas an average may be distorted.  The average conformation may  
never be sampled in reality even if each of the conformations  
contributing to the average do exist.  Thus, I like your last option  
the best.  However, factors to consider are the dispersion of the  
ensemble, the averaging method, whether the average has been  
minimized, and how similar the representative is to the average.

You may also wish to consult the literature and see what others have  
done in similar situations.
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 Jan 29, 2008, at 12:24 PM, Rachel Scherer wrote:

> Given that chimera doesn't calculate average NMR structures, this  
> query
> may be outside the groups interests, but can anyone suggest what the
> appropriate protocol is
>  when making aa-substitutions into an NMR structure:
> should an "average" be calculated (by averaging the atom coordinates
> across all the models in a PDB file that predates inclusion of the
> average into the database entry)
> or, should one use a representative from a cluster generated with
> "ensemble cluster" be chosen? Or an average of the representatives of
> the clusters?
> Or, the cluster representative that best matches the calculated  
> average?
> --
> Rachel Scherer			rachel at bio.umass.edu
> Biology Department		(413)545-2825	vox
> UMASS Amherst			(413)545-3243	fax

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