Alternate conformer clash problem in phenix.refine
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++ 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:[email protected]]
Aaron
Can you send me the files. The x-ray data is not required for debugging.
Cheers
n++
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Mon, Nov 19, 2018 at 2:57 PM Aaron Oakley
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++
*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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
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++
participants (3)
-
Aaron Oakley -
Nigel Moriarty -
Pavel Afonine