[phenixbb] Occupancy refinement of secondary conformation doesn't add up to 1.00

Benjamin Stauch bs448c at gmail.com
Sat Jun 14 12:46:14 PDT 2014

Hi Pavel,

many thanks, and great guess - there is indeed a TER between two
conformers. I imagine deleting this will solve my problem. As for my second
question, probably I would need to do something along the lines of example
#4 in your link and define a constrained_group?



2014-06-14 21:36 GMT+02:00 Pavel Afonine <pafonine at lbl.gov>:

> Hi Ben,
>  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:
> http://phenix-online.org/documentation/reference/
> refinement.html#occupancy-refinement
> Pavel
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