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@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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