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