Ed

You can use an edits. You can use the slack option to create a flat bottomed well which will allow the bond to be any value of distance_ideal plus/minus slack. The sigma curve starts at the border of the slack region.

I have given the example from the on-line docs below.

Cheers

Nigel


refinement.geometry_restraints.edits {
  zn_selection = chain X and resname ZN and resid 200 and name ZN
  his117_selection = chain X and resname HIS and resid 117 and name NE2
  asp130_selection = chain X and resname ASP and resid 130 and name OD1
  bond {
    action = *add
    atom_selection_1 = $zn_selection
    atom_selection_2 = $his117_selection
    symmetry_operation = None
    distance_ideal = 2.1
    sigma = 0.02
    slack = None
  }


On Fri, Apr 19, 2013 at 1:08 PM, Edward A. Berry <BerryE@upstate.edu> 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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Nigel W. Moriarty
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