[buster-discuss] Maintaining ligand planarity during refinement

[Andrew Sharff]

I am currently investigating!


Andrew


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
UK
Tel: +(0)1223 353033
Fax: +(0)1223 366889
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.globalphasing.com/pipermail/buster-discuss/attachments/20180131/e636324f/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 9478 bytes
Desc: not available
URL: <http://www.globalphasing.com/pipermail/buster-discuss/attachments/20180131/e636324f/attachment-0001.png>