[buster-discuss] Maintaining ligand planarity during refinement

Ashley Pike ashley.pike at sgc.ox.ac.uk
Wed Jan 31 15:41:20 CET 2018

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.


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)
[cid:image001.png at 01D39AA0.45EE8220]

Dr. Ashley Pike
Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford
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