[phenixbb] refining multiple conformations

Pavel Afonine pafonine at lbl.gov
Tue Aug 7 19:41:35 PDT 2012

Hi Kendall,

why don't you just define one stretch of the chain as conformer A, and 
the other one as conformer B, and then request that the occupancies of A 
and B add up to 1, by defining

refinement {
   refine {
     occupancies {
       constrained_group {
         selection = chain A and resseq 1:10 and altloc A
         selection = chain A and resseq 1:10 and altloc B


If you don't do this but let the default behavior then the altloc 
pairing will be done per residue and I guess you don't want this in your 


On 8/6/12 7:52 AM, Kendall Nettles wrote:
> Hi,
> We have a structure with the ligand showing two overlapping 
> conformers. When we refine it with both conformers separately, it is 
> pretty clear that there are substantial differences in the protein as 
> a result, for about a third of the protein chain. My question is, 
> would it be better to try to define altloc for those specific regions, 
> or would it be OK to refine with two entire alternate protein chains? 
> There is also a second protein chain that shows only a single binding 
> mode for the ligand.  It's a 2.0 angstrom structure with 4000 atoms 
> and 27,000 reflections. The yellow map goes with the green model in 
> the attached pic. Also, do we want to let each amino acid have its own 
> occupancy? or should one ligand copy and one chain all have the same 
> occupancy? I'm leaning towards the latter since the differences should 
> be directly tied to the ligand binding mode.
> Kendall Nettles

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