[phenixbb] Constraining carbohydrate conformation

Nigel Moriarty nwmoriarty at lbl.gov
Thu Aug 19 09:25:37 PDT 2010


The get the restraints file that the refinement used


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.


On Thu, Aug 19, 2010 at 8:50 AM, Ralf W. Grosse-Kunstleve
<rwgk at cci.lbl.gov> wrote:
> 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
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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