Hi Brandon, There is a small hint here: https://www.phenix-online.org/documentation/reference/refinement.html#defini... 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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]