[phenixbb] Planarity restraint ignored when dist_esd equal to 0

Nigel Moriarty nwmoriarty at lbl.gov
Tue Sep 27 09:48:51 PDT 2016


Here is a 3pg PDB file and a CCP4 restraints file.

I should point out that Phenix applies the planar esd individually to each
atom in the plane allowing some atoms to be more out of plane than others.
I'm working on using this feature to better advantage at the moment.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Sep 27, 2016 at 8:35 AM, Keitaro Yamashita <
k.yamashita at spring8.or.jp> wrote:

> 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,
> Keitaro
>
> 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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