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
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? ______________________________**_________________ phenixbb mailing list [email protected] http://phenix-online.org/**mailman/listinfo/phenixbbhttp://phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov