[phenixbb] Planarity restraint ignored when dist_esd equal to 0

Paul Adams pdadams at lbl.gov
Tue Sep 27 19:27:57 PDT 2016

It is my understanding that Refmac doesn’t make use of the CONST_X torsions in refinement either (I’d be very happy to hear more about this topic). In the monomer library files the planarities are defined by planes, so there is a redundancy in information. I think the CONST_X torsions are there for reporting but not for restraining (as they would be constraints by implication). If Phenix stopped because of torsions with 0 esd it would stop with all monomer library files with CONST_X records. We could report that they are there and not being used maybe. If someone defines an esd of 0 for a variable torsion then that might be a good place to throw an exception.

> On Sep 27, 2016, at 6:19 PM, Takanori Nakane <takanori.nakane at BS.S.U-TOKYO.AC.JP> wrote:
> Dear Pavel,
> I have recently encountered a similar situation, where I
> took a CIF file for a ligand from the CCP4 monomer library
> and found planarity restraints are silently ignored in PHENIX.
> This is very confusing and dangerous.
> > with this logic you interpret the number and not use it. Follow this
> > road you may end up with odd things, like let's treat 0 as
> > "constraints", 0.1 as "strong restraints", 1.5 as "weak restraints", etc
> > and in each case do something very different - I hope you get the idea.
> The "zero sigma" limit of a Gaussian is an infinitely sharp
> probability distribution (= delta function). So I think the transition
> from restraints to constraints is not "odd" but quite natural both
> mathematically and semantically.
> Anyway, if PHENIX does not want to treat 0 as constraints,
> I would prefer an error stop, not just a warning, because most people
> don't mean "ignore this record" by zero sigma.
> Takanori Nakane
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Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

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