# [phenixbb] occupancy refinement

Pavel Afonine pafonine at lbl.gov
Thu Nov 25 13:09:22 PST 2010

```  Hi Nat,

the way it's implemented currently: you can't add constraints on top of
another constraints. I'm not aware of any existing program that can do
it, although technically it's easy to implement.

However, Dalibor can do what he wants (if I understand two previous
emails correctly). In fact, phenix.refine will do it automatically, so
there is no need to even do anything special.

Pavel.

On 11/25/10 11:08 AM, Nathaniel Echols wrote:
> On Thu, Nov 25, 2010 at 10:26 AM, Pavel Afonine <pafonine at lbl.gov
> <mailto: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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