On Tuesday, March 27, 2012 04:35:40 pm Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> >phenix.refine allows any number of alternate conformers.
>
> Hmm..... quoting our old friends from the validation circuit: Where freedom
> is given, liberties will be taken....
True, but...
[warning: back of the envelope calculation]
Consider, for example, an isoleucine sidechain.
It would require 12 positional parameters to refine the position of
each sidechain atom (XYZ * {CB CG1 CG2 CD1}) for a single conformation.
One the other hand there are only 7 rotamers in the library.
So if you limited the refinement to the relative occupancy of the
7 ideal rotamers, that is a more parsimonious model than refining
the individual atoms for one conformation.
Season to taste with arguments about geometry restraints, but still
I think the liberty being offered is not so dangerous.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
