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

[Kendall Nettles]

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?
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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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