Hi Elliot,

Looking to generate restraints for phenix.refine that are similiar/equivalent to external restraints in REFMAC. From over viewing the documentation i feel the correct way to do this is to generate bond restraints, i.e:

Equivalent of:

exte dist first chain A resi 38 atom C alte A second chain A resi 38 atom C alte B value 0.0 sigma 0.02 type 1

would be :

I don't know how restraints function in Refmac.

refinment.geometry_restraints.edits {
    bond {
                          action = *add
                            atom_selection_1 = chain A and resid 38 and altloc A and name C
                            atom_selection_2 = chain A and resid 38 and altloc B and name C
                            symmetry_operation = None
                            distance_ideal = 0.0
                            sigma = 0.02
                            slack = None
                }
}

This will define a bond between these two atoms by adding a term to the restraints:

(1/sigma**2)*(distance_model - distance_ideal)**2

Note, you can add as many of such bonds as you with. Also, using similar syntax you can add angles, planes, torsions, etc.

Just out curiosity and if it's not a secret: what are you trying to achieve?

Pavel