[Chimera-users] average vs ensemble

Rachel Scherer rachel at bio.umass.edu
Tue Jan 29 12:24:27 PST 2008

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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