[phenixbb] constrained occupancy groups in phenix.refine

Pavel Afonine pafonine at lbl.gov
Fri Sep 3 14:42:07 PDT 2010

  Hi Lionel,

> A portion of my structure have two conformations at an interface 
> between two (NCS) protein chains -in addition to other alternates 
> conformations elsewhere.
> In both chains, I defined alt_A as one conformation and alt_B as the 
> second conformation, and also for the waters in this region.
> I would like to constrained the occupancy of these conformations.
> I though that the following selections would do the job:
> occupancies {
>       constrained_group {
>         selection = "(chain A or chain B) and (resseq 105 or resseq 
> 110:112 or resseq 140:143) and altid A"

yes, Nat is correct: you need to define two selections - one for 
altloc_A and the other one for altloc_B:

occupancies {
       constrained_group {
         selection = "chain A and resseq 105 and altloc A"
         selection = "chain B and resseq 105 and altloc B"

Essentially, the above selection tells: "alternative conformation A of 
residue 105 in chain A is coupled with alternative conformation B of 
(NCS related) residue 105 in chain B". The sum of refined occupancies 
will be 1 in this case. It is essential that altlocs in both selections 
are different - this turn the non-bonded interaction off so the residues 
will get pushed apart.

If you still having problems with this then please send me your PDB file 
and explain what should be constrained to what, and I will send you the 
working solution.

I'm not sure I understood your question about waters.


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