[phenixbb] occupancy refinement

Dalibor Milic dmilic at chem.pmf.hr
Thu Nov 25 14:05:55 PST 2010


On Čet, studeni 25, 2010 20:08, Nathaniel Echols wrote:
> On Thu, Nov 25, 2010 at 10:26 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
>> Although I see that occupancy of "AGLU A 30 " = occupancy of "AALA A 451
>> ",
>> it is not guaranteed in refinement, since otherwise that would be a
>> double-constrained refinement:
>>
>> constraint #1: occupancy(AGLU A 30) + occupancy(BGLU A 30)=1
>> constraint #2: occupancy(AGLU A 30) = occupancy(AALA A 451)
>>
>> which is not currently available.
>>
>
> Wait, now I'm confused too - isn't this the entire point of the
> constrained_group setting?  For example, the parameters below:
>
> refinement.refine.occupancies.constrained_group {
>   selection = "chain A and resseq 30"
>   selection = "chain A and resseq 451"
> }
>
> If both selections have alternate conformers A and B, and the occupancies
> for A and B are both 0.5, what would phenix.refine do?

I tried:

refinement.refine.occupancies.constrained_group {
    selection = "(chain A and resseq 30) or (chain A and resseq 451)"
  }

and got the same occupancy for both altLoc identifiers, i.e.

occupancy(AGLU A 30) = occupancy(BGLU A 30) = occupancy(AALA A 451) =
occupancy(BALA A 451)

and that is not what I wanted to get. Was I doing something wrong?

Regards,
Dalibor

-- 
Dalibor Milic
Laboratory of General and Inorganic Chemistry
Department of Chemistry
Faculty of Science
University of Zagreb
Horvatovac 102a
HR-10000 Zagreb
Croatia

phone:  +385 1 460 6377
fax:    +385 1 460 6341
e-mail: dmilic at chem.pmf.hr




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