[phenixbb] Constraining carbohydrate conformation

[Ralf W. Grosse-Kunstleve]

Hi Kenneth,

> I wonder how I can constrain the conformation of a NAG-residue during
> refinement. I have a dataset to 4.2 Angstrom. After refinement some
> sugars end up in the boat conformation. I would like to run the
> refinement so that the Asn side chain and the Asn-NAG linkage is
> refined (using xyz or torsion angle dynamics) but that the NAG-residue
> itself is considered as a rigid group.
>
> Maybe one way of doing this is constraining the bonds and angles of
> the NAG residue by the defining them as "custom bonds and angles" with
> sigma=0?

sigma=0 means phenix.refine will ignore the restraints completely.
We don't have algorithms that could use sigma=0.
We also don't have the combination of torsion-angle parameterization
and restraints that you are looking for.
But I think it would most likely not make a big difference anyway
(although it could be very convenient to use).
You can efficiently enforce a desired conformation by adding
dihedral restraints.

> Is there a possibility in phenix to generate these
> constraints from an ideal NAG-residue automatically?

phenix.reel could be useful here. You can start with the restraints
generated by elbow, then add dihedrals interactively to enforce
the desired conformation.

Ralf