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

Edward A. Berry BerryE at upstate.edu
Fri Apr 19 18:41:58 PDT 2013

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"<BerryE at upstate.edu>  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<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?
>>>     _________________________________________________
>>>     phenixbb mailing list
>>>     phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
>>>     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 : NWMoriarty at LBL.gov
>>> Fax   : 510-486-5909       Web  : CCI.LBL.gov<http://CCI.LBL.gov>
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