[phenixbb] Planarity restraint ignored when dist_esd equal to 0
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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