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

Nigel Moriarty nwmoriarty at lbl.gov
Fri Apr 19 16:07:21 PDT 2013


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.



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 at 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
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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