[Chimera-users] average vs ensemble

[Rachel Scherer]

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