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

[Nigel Moriarty]

Your understanding is correct.


On Fri, Apr 19, 2013 at 4:22 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?
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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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-- 
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
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