[phenixbb] Phenix.refine ignores ligand planarity restraint
Phil Jeffrey
pjeffrey at princeton.edu
Tue Feb 28 09:16:48 PST 2017
If restraint weighting is 1/sigma^2 then setting sigma=0.0 may produce
some interesting results. I suspected that setting them to zero might
turn the restraints off but can't find a reference to support that.
phenix.refine writes a .geo file that lists geometry restraints and
sorts them within the file by residual (presumably weighted deviation).
That's the first place I'd go look for outliers resulting from your
definition of the geometry and compare residuals before/after refinement
for what terms are being minimized at the expense of others.
Phil Jeffrey
Princeton
On 2/28/17 11:44 AM, Maike Bublitz wrote:
> Dear all,
>
> thank you again for all your suggestions. Here’s what I’ve tried,
> without success:
>
> 1) reduce deviation from planarity restraints to very small value or
> zero -> ligand still gets distorted in refinement
>
> 2) Set all bond angle restraints to ideal values and checked sums of
> angles in planar rings -> ligand still gets distorted in refinement
>
> 3) Used phenix.elbow with - -final-geometry on a pdb of a planar ligand
> —> ligand still gets distorted in refinement
>
> 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”.
>
> Does anyone have another suggestion, except for installing an extra QM
> package?
>
> Best,
> Maike
>
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