[phenixbb] Phenix.refine ignores ligand planarity restraint
pafonine at lbl.gov
Tue Feb 28 09:11:03 PST 2017
could you please send me input files and I will provide the solution for
> 1) reduce deviation from planarity restraints to very small value or
> zero -> ligand still gets distorted in refinement
Setting esd to very small number means huge contribution of that
restrain to refinement target because corresponding weight is 1/esd**2.
So I'm not surprised it did not work.
> 2) Set all bond angle restraints to ideal values and checked sums of
> angles in planar rings -> ligand still gets distorted in refinement
You need a plane and phenix.refine allows you to put any desired atoms
into a plane, so no need to work-around this using angles.
> 3) Used phenix.elbow with - -final-geometry on a pdb of a planar
> ligand —> ligand still gets distorted in refinement
I hoped Nigel addresses this one.
> 4) Used the grade server (grade.globalphasing.org
> <http://grade.globalphasing.org>) to generate cif file from SMILES
> string—> phenix.refine stops with message “Unknown file format:
External to Phenix tools do not guarantee to provide inputs good for Phenix.
> Does anyone have another suggestion,
See above: send me files and I will make it work.
> except for installing an extra QM package?
QM in this particular case would be a "cannon to kill a fly".
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