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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