[phenixbb] Refining structure with overlapping conformations of different residues

Pavel Afonine pafonine at lbl.gov
Thu Sep 18 23:52:16 PDT 2014

Hi Igor,

yes, it is possible to do this in phenix.refine. There are several ways 
of doing this that are described here:


Also, you can send me PDB file and I will make sure things work as desired.


On 9/18/14 1:30 PM, Igor Petrik wrote:
> Hi,
> I am trying to refine a structure in which there are two sets of 
> linked conformations of two residues. Around half of the occupancy 
> (altloc A) corresponds to the sidechain of residue 29 pointing into 
> the pocket and residue 65 pointing out and the other conformation 
> (altloc B) has the side chain of residue 65 in the pocket (where 
> residue 29 is in altloc A) and residue 29 pointing out of the pocket. 
> I am refining them by using occupancy refinement groups in, but phenix 
> refine seems to think that altloc A of residue 29 and altloc B of 
> residue 65 may exist at the same time and pushes them apart to avoid 
> clashes. Is there any way around this?
> - Igor

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