[phenixbb] Local restraints

[Tomas Malinauskas]

Hi Luca,

Yes, it is for a disulphide in this example but it works for other atoms, too.

Best wishes,
Tomas

On Tue, Mar 7, 2023 at 11:07 AM Luca Pellegrini <lp212 at cam.ac.uk> wrote:
>
> 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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