[phenixbb] occupancy refinement

Nathaniel Echols nechols at lbl.gov
Thu Nov 25 11:08:27 PST 2010


On Thu, Nov 25, 2010 at 10:26 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> In the example below I see residue #30 has two conformations, A and B, and
> they are automatically constrained-refined in phenix.refine and their sum
> adds up to 1 (0.52+0.48).
> Same for residue #451.
>
> 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?

-Nat
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