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

Edward A. Berry BerryE at upstate.edu
Fri Apr 19 16:22:35 PDT 2013


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 <BerryE at upstate.edu <mailto: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 <http://CCI.LBL.gov>
>
>
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