On Tue, Feb 24, 2009, Sally Pias wrote:
>
> I have a follow-up question related to the use of ambiguous restraints
> in NMR refinement of a dimeric protein structure. In addition to
> commonly occurring ambiguities, I have introduced an ambiguity for
> every distance restraint, representing a scenario where it is possible
> that a given restraint could involve two atoms/groups on a single
> protomer OR one atom/group on the first protomer and one on the second
> protomer. My question is whether it is appropriate to correct for
> r**-6 averaging due to these "protomer-protomer" ambiguities. The
> correction has already been applied to other ambiguities in the
> distance restraints list.
It depends on where the constraints come from, and what they will be
used for. The r**-6 averaging comes from NMR, where it is physically
correct to view an observed (ambiguous) NOE peak as being a weighted sum
of two or more unresolved peaks, that contribute with an r**-6 average.
This functional form also has the advantage that nearby contacts are
heavily weighted and distant ones are effectively ignored. If this is
what you want, then you should give it a try--it's mostly like an "OR"
restraint, but not exactly.
...hope this helps...dac
--
================================================================
David A. Case | email:
BioMaPS Institute and Dept. of | case.biomaps.rutgers.edu
Chemistry & Chemical Biology | fax: +1-732-445-5958
Rutgers University | phone: +1-732-445-5885
610 Taylor Rd. |
Piscataway, NJ 08854-8087 USA | http://casegroup.rutgers.edu
================================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 25 2009 - 01:19:46 PST
