> the liberty being offered is not so dangerous
Parameter-wise, true, - if it is understood that you are now *modeling with
little evidence*.
How much electron density to affirm your model choices would one expect at
say 7 ideal rotamers - which on top of static split will likely display
dynamic motion?
On the other hand, the side chain HAS to be somewhere, and a distribution of
the most probable rotamers with their respective frequencies may be more
realistic
than all other options (as long as the lack of specific experimental
evidence is acknowledged).
But overall, that model might be better due to the more reasonable prior
expectation term
although the R-value will be practically unaffected due to the lack of
localized scattering contributions.
Anyhow, if it can be abused, it will be ;-)
Best BR
-----Original Message-----
From: Ethan Merritt [mailto:[log in to unmask]]
Sent: Tuesday, March 27, 2012 5:14 PM
To: [log in to unmask]
Cc: [log in to unmask]
Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry
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
