[phenixbb] refining multiple conformations

[Pavel Afonine]

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 
case.

Pavel

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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