[phenixbb] Constraining carbohydrate conformation

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Aug 19 08:50:11 PDT 2010

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.


More information about the phenixbb mailing list