[phenixbb] Alternate conformer clash problem in phenix.refine

Aaron Oakley aarono at uow.edu.au
Mon Nov 19 14:54:49 PST 2018


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,


Aaron Oakley
Associate Professor
School of Chemistry and Molecular Bioscience | Molecular Horizons | Faculty of Science, Medicine and Health
University of Wollongong NSW 2522 Australia
T +61 2 4221 4347 | F +61 2 4221 4287

[cid:A97921CB-CF5B-448D-BCF6-E988D0A95C12 at ad.uow.edu.au]

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