AMBER Archive (2009)

Subject: Re: [AMBER] follow-up to previous discussion: nmr refinement of dimer

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Feb 24 2009 - 07:15:27 CST

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 

-- 

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David A. Case                     | email:                      
BioMaPS Institute and Dept. of    |     case_at_biomaps.rutgers.edu
    Chemistry & Chemical Biology  |    fax:      +1-732-445-5958
Rutgers University                |    phone:    +1-732-445-5885
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