[phenixbb] Phenix.refine ignores ligand planarity restraint

[Dale Tronrud]

   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>
> 
> 
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