[phenixbb] Local restraints

[Luca Pellegrini]

Hi Tomas,

Thank you for your help. Is this for restraining a disulphide bond? I am actually looking for a way to keep a side chain from moving during refinement.

Best wishes
Luca


> On 7 Mar 2023, at 11:00, Tomas Malinauskas <tomas.malinauskas at gmail.com> wrote:
> 
> Hi Luca,
> 
> I typically create a file called restraints.eff containing something like
> 
> refinement {
>  geometry_restraints.edits {
>    bond {
>      atom_selection_1 = (chain 'A' and (resid 101 and (name SG )))
>      atom_selection_2 = (chain 'A' and (resid 102 and (name SG )))
>      distance_ideal = 2.03
>      sigma = 0.1
>      slack = 0
>    }
>  }
> }
> 
> and simply load this file via Phenix GUI. I am not sure if that is
> what Phenix developers recommend. I would be curious to know, too.
> 
> Best wishes,
> Tomas
> 
> On Tue, Mar 7, 2023 at 10:44 AM Luca Pellegrini <lp212 at cam.ac.uk> wrote:
>> 
>> How can I freeze a set of atoms in phenix.real_space_refine? I've got an arginine side chain that is consistently misplaced during refinement, and I’d like to restrain its movement. I notice that refinement.geometry_restraints.edits.scale_restraints  is not available anymore, is there another way?
>> 
>> Thanks,
>> Luca
>> 
>> Luca Pellegrini, PhD
>> Department of Biochemistry
>> University of Cambridge
>> Cambridge CB2 1GA
>> UK
>> 
>> 
>> 
>> 
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