[Xplor-nih] SA with backbone j-coupling restraints

[John Kuszewski]

Hi Andrew,

Yes, translating 3J couplings into rough torsion angle restraints is  
standard practice.
Anything to remove false minima is a good idea.  Note that Gabriel  
Cornilescu's TALOS
can often do this automatically for you for the backbone torsions,  
since TALOS's
predictions are right 98% of the time.

The advantage of including the 3J couplings directly as restraints is  
in cleaning up
the final torsion angles as much as possible.  It's a refinement  
tool, not a structure
determination tool.

And since very small systems often have very few NOEs, pushing your  
3J information
as far as it can go is obviously valuable.

--JK

On Aug 15, 2007, at 9:56 PM, Andrew Borgert wrote:

> Thanks for the input, it was very helpful.
>
> I'd like to extend this discussion a bit if that's alright.  I've
> noticed in several papers that people translate j-coupling values into
> dihedral restraints in an effort (presumably) to avoid the problem of
> multiple karplus solutions.  For example, a coupling greater than 8 Hz
> is translated to a phi dihedral of -140 +/- 40, even though +140 is  
> also
> a valid solution to the karplus equation (granted that +140 is out in
> the no-mans land of the Ramachandran plot).  Is this sort of thing
> considered standard practice?  Is it even worth doing on a small  
> system
> (15 residues)?
>
> Thanks
>     Andrew Borgert