Constraining carbohydrate conformation
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
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
Ken
The get the restraints file that the refinement used
$PHENIX/chem_data/mon_lib/n/NAG-B-D.cif
Copy the file to your local directory, edit with REEL (or by hand)
phenix.reel NAG-B-D.cif
and edit the dihedral ESD to a value of about 1. Any smaller and you
will have weighting issues.
Supply the new cif to the phenix.refine.
Nigel
On Thu, Aug 19, 2010 at 8:50 AM, 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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participants (3)
-
Kenneth Verstraete -
Nigel Moriarty -
Ralf W. Grosse-Kunstleve