[phenixbb] Phenix.refine Restraints: replicating refmac external restaints

Elliot Nelson elliot.nelson at dtc.ox.ac.uk
Wed Jan 18 09:37:31 PST 2017

Hi All,

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 :

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

If this is incorrect: Am i missing another way to create external restraint functionality in phenix, or am I making a more fundamental misunderstanding of how restraints are handled in both programs?

Thanks in advance

Elliot Nelson
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