NAD & b-factors > 100A2

chemjjt at SHOWME.MISSOURI.EDU chemjjt at SHOWME.MISSOURI.EDU
Mon Jul 21 16:50:34 EST 1997


I guess the bfactors are high because the model is out of density.

Are you sure you have the NAD force field parameters set up correctly
after you modified the naming convention?

If one of the terms, eg vdw, is messed up then xplor might move
the NAD out of density to satisfy the vdw force.  You might look
to see if any of the xplor energy components changes significantly
during refinement.  You could also try several runs in which 
various energy terms are omitted from the refinement.

Jack Tanner

--------------------------------------------------------------------------
Dr. John J. Tanner
University of Missouri - Columbia
Chemistry Department
211 Chemistry Bldg.
Columbia, MO  65211

phone 573-884-1280
fax   573-882-2754

chemjjt at showme.missouri.edu
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On Mon, 21 Jul 1997, Jordi Benach wrote:

> Dear x-plor users,
> 
> I'm refining a structure of a complex at 2.6 A resolution. The enzyme
> is complexed with NAD and an inhibitor. And one can see clearly the
> molecule of NAD+ in Fo-Fc maps without any problem.
> 
> In order to avoid problems with "O". I renamed the atoms in the NAD+
> molecule to my own ones (like C1, C2, .. N1, N2... O1, O2... etc)
> and change the corresponding xplor topology.nad file.
> 
> Then I divide the molecule in several pieces to fit easier the molecule
> into the density.
> 
> Do model building and assemble the pieces to a single regular NAD+
> molecule, finally do some positional refinement cycles.. it usually
> refines the molecule away from the electron density.(??? I wonder)
> 
> When I do group b-factor refinement of the NAD+ molecule, the value
> gets about 100 A2? If I try individual b-factor refinement -only for
> the NAD+ molecule- some atoms get as well 100 A2 as b-factor.
> 
> Could someone give me a hint?
> 
> Thanks,
> 
> JB
> 
> 




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