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

Pavel Afonine pafonine at lbl.gov
Mon Apr 22 07:47:39 PDT 2013

Hi Ed,

ok, this makes me feel better about this -:)

All the best,

On 4/22/13 7:46 AM, Edward A. Berry wrote:
> 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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