[phenixbb] Occupancy refinement of secondary conformation doesn't add up to 1.00
pafonine at lbl.gov
Sat Jun 14 12:36:52 PDT 2014
> I do a refinement of a glycoprotein that has a NAG-NAG attached to an
> Asn. The data set is very high resolution and I am positive there is
> indication of a secondary conformation of the entire attachement.
> I modeled a second conformation in Coot and run my refinement, with
> the "adjust occupancy" option checked. After initially setting both
> occupancies to 0.5, I am puzzled to see one of the NAGs to be refined
> to 0.45 (conformer A) and 0.75 (conformer B) occupancy .. For the
> other NAG, and indeed all amino acid residues, things always add up
> like they should.
> Additionally to this, I was wondering if there was an easy option to
> restrain each conformer of the entire Asn-NAG-NAG group to have
> uniform occupancies -- i.e. the Asn and both NAGs of conformer A to
> have identical occupancy.
I'm pretty sure the problem stems from incorrectly formatted PDB file
(perhaps TER records inserted between conformations/residue, etc..). If
you send me PDB file or just a fraction of it with residues/ligands in
question I will tell what exactly is the root of the problem.
More information about how phenix.refine does occupancy refinement:
More information about the phenixbb