[buster-discuss] Maintaining ligand planarity during refinement

Marco BELLINZONI marco.bellinzoni at pasteur.fr
Wed Jan 31 19:33:34 CET 2018

Dear Ashley,

we have also run across the same problem with planarity, and at higher resolutions. The only workaround we found (actually suggested to me by a colleague) was to raise the overall weight of planarity restraints, by adding:


As in Ashley’s case we originally noticed that with some ligands (e.g. uridine ring in UTP), but the issue does not seem to be restricted to ligands with externally provided dictionaries, as we have sometimes seen aromatic side chains also refining slightly out of plane, most likely as an effect of anti-bumping restraints. Indeed, in the few tests I made on parallel refinements with or without the instruction above I’ve seen that applying such a higher weight to planarity worsens Molprobity clash scores, although not dramatically.

Is there a better way to deal with this, or possibly strengthen this kind of restraints for a particular ligand instead of the whole model (e.g. Gelly instructions)?

Thanks in advance,

On 31 Jan 2018, at 15:41, Ashley Pike <ashley.pike at sgc.ox.ac.uk<mailto:ashley.pike at sgc.ox.ac.uk>> wrote:

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)

Dr. Ashley Pike
Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford
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Marco Bellinzoni
Unité de Microbiologie Structurale
Institut Pasteur
25, rue du Dr. Roux
75724 Paris Cedex 15
Tel: +33 (0)1 45688608
Fax: +33 (0)1 45688604

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