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 mailto:[email protected]> 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.ukhttp://bioch.ox.ac.uk/
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