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

Ed and Nigel, we have done a lot of liganded structures with Phenix including thiophenes and have not turned off non-bonded interactions before. Im curious, what would be the benefit and when would you do this? Best regards Kendall On Apr 19, 2013, at 4:23 PM, "Edward A. Berry" wrote:

I see. So if distance_ideal is 3.0 and slack is 0.3, then anywhere between 2.7 and 3.3 will be equal in energy as far as the restraints go? I can see that would better than setting a huge sigma. Thanks, Ed

Nigel Moriarty wrote:

...

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 mailto:[email protected]> 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? _________________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/__mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb

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