[phenixbb] Planarity restraint ignored when dist_esd equal to 0

Keitaro Yamashita k.yamashita at spring8.or.jp
Tue Sep 27 08:35:27 PDT 2016

Dear Pavel,

Yes, it would be problematic if 0 is not treated specially. What we
normally expect might be the planarity constraint if sigma is 0. I
don't know how ccp4 treats it (for example refmac5 keeps atoms planar
in this case), but maybe just the value of the first atom is used?

Thank you very much for your help but I am sorry that I cannot give a
PDB file because I do not have it.. Could you please generate a test
data yourself?

Best regards,

2016-09-28 0:23 GMT+09:00 Pavel Afonine <pafonine at lbl.gov>:
> 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

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