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

Benjamin Stauch bs448c at gmail.com
Sun Jun 15 05:51:24 PDT 2014


Just for anyone's reference, adding a occ.params file with the following
content,

refinement {
  refine {
    occupancies {
      constrained_group {
        selection = chain A and (resseq 74 or resseq 401 or resseq 402) and
altloc A
        selection = chain A and (resseq 74 or resseq 401 or resseq 402) and
altloc B
      }
    }
  }
}

(where 401 and 402 are the NAGs and 74 the Asn they're conjugating) was
what I was looking for.


2014-06-14 21:46 GMT+02:00 Benjamin Stauch <bs448c at gmail.com>:

> 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?
>
> Thanks!
>
> Ben
>
>
> 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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