Hello Marie-Laurence--
>
> Our lab recently switched from XPLOR-NIH version 2.19 to version
> 2.33. ?It would seem that the former proton stereospecificity (HD**
> or HG**) in the NOE restraint files have changed to only accept HD(1
> or 2)* or HG(1 or 2)*.
I apologize. This is a bug- it will be fixed in the next
release. However, you should be able to use simply HD* or HG* in this
case.
> My methyl protons aren't stereospecifically assigned and I was
> wondering how XPLOR is treating those proton and how we keep the
> ambiguity?
sum averaging is usually used, which usually effectively picks out the
shortest distance.
> Do we have to use the potential
> described in:
>
> Kuszewski, J., Gronenborn, A.M. & Clore, G.M. (1996) A potential
> involving multiple proton chemical shift restraints for
> non-stereospecifically assigned methyl and methylene
> protons. J. Magn. Reson. Series B 112, 79-81
That algorithm is not implemented for distance restraints, and I'm not
convinced it will work particularly well. Sum averaging is probably a
better bet.
best regards--
Charles
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Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
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