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 phenix.refine" http://phenix-online.org/newsletter/ Pavel 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++