[phenixbb] Phenix.refine ignores ligand planarity restraint

Tanner, John J. TannerJJ at missouri.edu
Mon Feb 27 09:12:08 PST 2017

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,

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

phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
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>

More information about the phenixbb mailing list