[phenixbb] constrained occupancy groups in phenix.refine

Young-Jin Cho yjcho at brandeis.edu
Fri Sep 3 08:47:21 PDT 2010

In my case, if you look at the pdb file, check if there is 'TER' between alt_A and alt_B residues. Once you got rid of 'TER', the sum of occupancy should be 1 finally.


On Sep 3, 2010, at 11:23 AM, Lionel Costenaro wrote:

> Hello, 
> 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"
> After refinement, all alt_A selected residues do have the same occupancy, but not the same occupancies for alt_B and the sum for one residue (occu alt_A +occu alt_B) is not 1.
> Adding a second group with the same selection but "altid B", constrains also the alt_B occupancies but the sum is still not 1.
> How should I defined my group(s)?
> Is it possible to select several non continuous residues from one chain (that's for the waters) without repeating each time "or resseq" ?
> Best regards, 
> Lionel
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