[phenixbb] Planarity restraint ignored when dist_esd equal to 0

Keitaro Yamashita k.yamashita at spring8.or.jp
Tue Sep 27 04:22:47 PDT 2016

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

At least, it would be helpful if phenix shows warning in this case.

Best regards,

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