[buster-discuss] Maintaining ligand planarity during refinement

Andrew Sharff asharff at globalphasing.com
Wed Jan 31 15:59:57 CET 2018

I am currently investigating!


On 31/01/18 14:41, Ashley Pike wrote:
> Hi,
> Does anyone have any tips to force buster to maintain planarity when 
> refining ligands. I am refining a UDP-GlcNAc (UD1) and the N1 of the 
> uracyl base is refining out of plane. Using the bigplanes option when 
> generating the cif helps a lot but the N atom is approx. 0.1A out of 
> the plane (compared to ideal or refmac refined). N1 is in same plane 
> as aromatic ring but not with C1 of ribose. How to I increase 
> weighting towards geometry for ligand – perhaps adding something to 
> gelly file to modify overall weight?
> Using the latest snapshot version of buster
> Resolution is 3.1A so perhaps I can’t expect anything better.
> FWIW the cif file used was generated by grade from the PDB ligand 
> entry. The cif file itself is fine as using to refine in coot or 
> refmac results in maintenance of planarity.
> Cheers,
> Ashley
> Lower buster-refined model shows N1 of uracyl ring out-of-plane wrt to 
> C1 atom of sugar on left-hand side (top models are coot-idealised and 
> refmac-refined)
> --
> Dr. Ashley Pike
> Membrane Protein Crystallography | Structural Genomics Consortium | 
> University of Oxford
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*Dr. Andrew J. Sharff D.Phil**
*Research Scientist / Software Developer
Global Phasing Ltd
Sheraton House
Castle Park
Cambridge CB3 0AX
Tel: +(0)1223 353033
Fax: +(0)1223 366889
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