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@upstate.edu <mailto: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
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty@LBL.gov

Fax   : 510-486-5909       Web  : CCI.LBL.gov <http://CCI.LBL.gov>

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