You could also check that the other restraints in your cif are
compatible with planarity. If the sum of the three bond angles for a
planar atom is less than 360 deg your angle restraints will be fighting
with your planarity. You also have to check the sum of the internal
angles of your planar rings. If I recall correctly the sum of the
internal angles must equal n*180 - 360 for the ring to be flat.
Dale Tronrud
On 2/27/2017 9:05 AM, Maike Bublitz 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
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: [email protected]
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe:
[email protected]