[phenixbb] Planarity restraint ignored when dist_esd equal to 0

Pavel Afonine pafonine at lbl.gov
Tue Sep 27 08:23:43 PDT 2016

Hi Keitaro,

> My colleague noticed that planarity restraint of a ligand was ignored
> when a cif file in CCP4 monomer library was given to phenix.refine.
> The cif file was $CLIBD_MON/3/3PG.cif.
> This was because phenix (mmtbx) ignores planarity restraint when
> dist_esd is 0. In the line 2055 of
> mmtbx/monomer_library/pdb_interpretation.py (phenix-1.10.1),
> plane_atom is not added to the list when (plane_atom.dist_esd in
> [None, 0]) is True.

yep, that's right. This is because restraints are T = SUM w*(p_model - 
p_ideal)**2, with w = 1/esd**2. So instead of bombing with division by 
zero error, the software ignores instances of restraints that would 
cause numeric troubles.

I agree a warning may be helpful! Could you please send me a PDB file 
that contains this ligand?


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