[phenixbb] Turn off non-bonded interactions to measure distance in case of unknown interaction

Pavel Afonine pafonine at lbl.gov
Mon Apr 22 00:19:04 PDT 2013

The only way to turn non-bonded repulsions between two atoms (without 
involving altlocs) is to define a bond between them, and Nigel's 
suggestion will let you tune it such that the bond may not actually act 
as such while disabling non-bonded repulsions. I see it's a bit indirect 
and rather hackish way of doing this, and it would be way nicer to have 
a functionality to just say "exclude these atoms from repulsions", but 
that's not implemented (yet), sorry.


On 4/19/13 1:08 PM, Edward A. Berry wrote:
> I have a phenix-specific question and a general chemistry question.
> In a ligand-bound structure, S in an aromatic ring (substituted 
> thiophene)
> may be H-bonding NH1 of arginine guanidino group.
> The general question is whether thiophene S can act as H-bond acceptor
> (assuming one lone pair is in the aromatic pi system for a total of 6 e,
> the other lone pair is available as H-bond acceptor?).
> The phenix-specific question involves whether non-bonded interactions
> will push the atoms apart during refinement, and how to turn off the
> nonbonded interaction between these two atoms to allow the xray data
> to determine the position.
> Under geometry_restraints.edits I define a bond, but give a very
> large sigma of 1A.
> Will this effectively remove non-bonded interactions between these
> two atoms?
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