[buster-discuss] Maintaining ligand planarity during refinement

Andrew Sharff asharff at globalphasing.com
Fri Feb 2 15:39:55 CET 2018

Dear Ashley,

Thank you for bringing this issue to our attention. We appreciate 
getting feedback / problem reports from users so we can ensure we 
continue to improve our software.

Your findings are a little unexpected but we have occasionally had 
reports about similar behaviour before.

Firstly, it is not at all surprising that you get behaviour closer to 
your expectation from a restraint dictionary from Grade using the 
-bigplanes options.  By default, Grade generates a series of overlapping 
4-atom plane restraints (as you will see if you look at the standard 
Grade UD1 dictionary).  There is also a good reason for doing it this 
way, since some (large) ring systems actually show real deviation from 
exact planarity (e.g. FAD) and by using a collection of small, 
overlapping planes we can handle this. Usually, this approach is quite 
sufficient to maintain planarity in rings. However, not always. The 
-bigplanes option sees overlapped 4-atom planes conflated (where 
appropriate) into a single, large plane. In this case, if you look at 
the bigplanes dictionary you will see a single plane restraint for the 
uracyl ring, including C1.

We have tried running BUSTER, with UD1 dictionaries generated a) with 
Grade, b) with Grade and -bigplanes and c) by CCP4, on a number of PDB 
structures that contain UD1 and thus far  we have been unable to 
reproduce your problem. Indeed, in one of the models we looked at, 4gx5 
(a 3.1A structure) the uracyl ring is non-planar in the deposited model 
but ends up completely planar after BUSTER (regardless of which 
dictionary I use).

The suggestion made to you by Marco Bellinzoni may well work but it is 
an approach that we would urge caution against using, at least at this 

We wonder if there is a more particular issue with the local environment 
around the UD1 that results in the C1 being forced out of plane of the 
uracyl ring? If the cause is some modelling problem, Marco's suggestion 
may lead to the planarity being maintained but may simply mask the root 
cause. His suggestion will also apply globally over the whole structure, 
not locally on the UD1.

What is the environment around the UD1? Are there any close contacts / 
residues that need to be resolved? What about alternate conformations?

Also, and despite the resolution, is your model (or just the UD1)  
hydrogenated - this may also have also have an impact on the refinement. 
Note that BUSTER does not use a "riding hydrogen" model as refmac does, 
it includes them in calculation of the geometric terms, so these could 
well be having an impact.

Would it also be possible for you to send us the model / mtz file so we 
can look at this directly.

Best wishes

Andrew and Clemens

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
> _______________________________________________
> buster-discuss mailing list
> buster-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/buster-discuss

*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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