[phenixbb] Imposing bond restraints across the asymmetric unit

[Oleg Sobolev]

Hi Brandon,

There is a small hint here:
https://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles

For bonds to symmetry copies, specify the symmetry operation in xyz
> notation, for example:
> symmetry_operation = -x-1/2,y-1/2,-z+1/2


The whole .eff file might look like:
 refinement.geometry_restraints.edits {
    bond {
      action = *add delete change
      atom_selection_1 = chain A and resid 1199 and name O4
      atom_selection_2 = chain A and resid 1196 and name C1
      symmetry_operation = X-1/2,-Y+1/2,-Z
      distance_ideal = 1.439
      sigma = 0.020
    }
}

Best regards,
Oleg Sobolev.

On Fri, May 22, 2020 at 3:55 PM Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Brandon,
>
> I have an unusual problem in which my enzyme (a dimer) is covalently bound
> to its own C-terminus and so is daisy-chained across the crystal lattice.
> In the past, I have encountered and fixed this problem by extracting the
> covalent part of the molecule and re-phasing using that as the molecular
> replacement model. In this case, I am not able to due so. When I input the
> restraints, it either crashes refine or attempts to impose them on the
> corresponding residues within the ASU (understandable) but they are quite
> distal and this leads to "interesting" refinement results. Is there a good
> way of making phenix.refine do what I want? Or perhaps a workaround that I
> haven't considered yet?
>
>
> this should be possible but I don't remember what it takes. If you send me
> the file I might be able to figure this out.
>
> Pavel
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