[phenixbb] Constraining carbohydrate conformation

Kenneth Verstraete kenneth.verstraete at ugent.be
Thu Aug 19 02:45:19 PDT 2010

Dear phenixbb users,

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

Thank you very much for you advice,

Kenneth Verstraete

More information about the phenixbb mailing list