[phenixbb] Phenix.refine ignores ligand planarity restraint

[Tanner, John J.]

You could try setting the deviation from planarity parameter to a very small value (maybe zero?).  It is the number after the atom name:

NAP plan-1    C6A 0.020



On Feb 27, 2017, at 11:05 AM, Maike Bublitz <maike.bublitz at bioch.ox.ac.uk<mailto:maike.bublitz at bioch.ox.ac.uk>> wrote:

Dear all,

this has probably been discussed many times before, but I just can’t seem to find a solution for my current problem with phenix.refine:

I am trying to refine a protein structure with a rather complex ligand. I’ve generated a .cif file for the ligand with eLBOW, including planarity restraints for its aromatic ring systems. However, phenix.refine keeps on distorting the 6-ring in my indole group, although all respective atoms are included in the plane definition.
At a resolution of 3.0 A, I’d very much prefer to impose an ideal planar structure on this ligand.

How can I convince Phenix to not distort my ligand's aromatic rings?

Many thanks for your kind suggestions.

Best regards,
Maike

*************************************************
Dr. Maike Bublitz
Associate Professor of Microbial Biophysics
Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU
United Kingdom
phone: +44 (0)1865 613221
lab: +44 (0)1865 613318
maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk/>










_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave at phenix-online.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170227/7368e9c4/attachment.htm>