[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

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

More information about the phenixbb mailing list