27 Sep
2016
27 Sep
'16
11:22 a.m.
Dear PHENIX developers, 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. _chem_comp_plane_atom.dist_esd in 3PG.cif (ccp4-7.0) is all zero except the first atom in the plane definition. As far as I checked, there is no cif file where dist_esd of the first atom of plane is zero. At least, it would be helpful if phenix shows warning in this case. Best regards, Keitaro