[phenixbb] Phenix.refine ignores ligand planarity restraint

Pavel Afonine pafonine at lbl.gov
Tue Feb 28 09:11:03 PST 2017

Hi Maike,

could you please send me input files and I will provide the solution for 
your issue?

> 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: 
> grade-ligand.cif”.

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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