[phenixbb] Alternate conformer clash problem in phenix.refine

Pavel Afonine pafonine at lbl.gov
Mon Nov 19 17:59:17 PST 2018

Hi Aaron,

have a look at this article that describes how to set up refinement for 
similar cases..

"13 typical occupancy refinement scenarios and available options in 


On 11/20/18 06:54, Aaron Oakley wrote:
> Salve!
> I am refining a protein/ligand complex where the ligand is bound with 
> two conformers.
> Conformer A is covalently bound to a cysteine residue.
> Conformer B is free.
> I have prepared an appropriate cif dictionary for the ligand including 
> info on handling the link.
> The problem is that during refinement, non-bonded interactions between 
> the two conformers appear to not be switched off and their geometry 
> becomes distorted.
> Is this diagnosis correct? If so, is there a way to manually switch 
> off interactions?
> With thanks,
> a++

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