[phenixbb] Planarity restraint ignored when dist_esd equal to 0

Takanori Nakane takanori.nakane at bs.s.u-tokyo.ac.jp
Tue Sep 27 18:19:27 PDT 2016

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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