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? Pavel