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

-- 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 http://CCI.LBL.gov

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In deciding what kind of interaction is going on, I wanted to know what the distance involved was. But I wasn't sure how the distance I measure in the refined structure would be affected by assumptions that phenix.refine was making- If there was really a hydrogen bond but phenix was applying non-bonded interaction, would that bias it to longer distances? But I am embarrassed to say the problem has gone away because it looks like the fit is better with the ring flipped, and what seemed to be shorter than sum of vanderwals radii with S is just fine with C there. Perhaps because of phase bias the density was ambiguous before, but maps calculated with the ring flipped show significantly stronger density in the new position of the S atom. May be worth trying to look at Bijvoet diff maps. Still the information about the "slack" term is good to know. Kendall Nettles wrote:

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. Berrymailto:[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/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.govhttp://CCI.LBL.gov

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

---

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Hi Ed, ok, this makes me feel better about this -:) All the best, Pavel On 4/22/13 7:46 AM, Edward A. Berry wrote:

I think this is a good and intuitive way to do it. If you don't do anything, phenix takes care of the interaction as best it knows how. If you define a bond, you are defining the interaction and overriding the automatic definitions. And one thing you can define is to have no interaction within a certain distance range, allowing the xray data to determine the position.

Pavel Afonine wrote:

...

The only way to turn non-bonded repulsions between two atoms (without involving altlocs) is to define a bond between them, and Nigel's suggestion will let you tune it such that the bond may not actually act as such while disabling non-bonded repulsions. I see it's a bit indirect and rather hackish way of doing this, and it would be way nicer to have a functionality to just say "exclude these atoms from repulsions", but that's not implemented (yet), sorry.

Pavel

On 4/19/13 1:08 PM, Edward A. Berry 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] http://phenix-online.org/mailman/listinfo/phenixbb