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

Edward A. Berry BerryE at upstate.edu
Mon Apr 22 07:46:04 PDT 2013

I think this is a good and intuitive way to do it.
If you don't do anything, phenix takes care of the interaction as best
it knows how. If you define a bond, you are defining the interaction
and overriding the automatic definitions. And one thing you can define is
to have no interaction within a certain distance range, allowing the
xray data to determine the position.

Pavel Afonine wrote:
> 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.
> Pavel
> 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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