[phenixbb] distance restraints

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Jul 2 13:35:55 PDT 2008

Hi Oliver,

> I am about to define distance restraints for a metal coordination site
> using a refinement.geometry_restraints.edits entry.  Unfortunately,
> two of the four ligand side chains come from a symmetry-related
> molecule! What is the syntax to properly refer to a symm in such
> a case?

You have to use the "symmetry_operation" keyword in this input block:

  refinement.geometry_restraints.edits {
    bond {
      action = *add delete change
      atom_selection_1 = None
      atom_selection_2 = None
      symmetry_operation = None
      distance_ideal = None
      sigma = None
      slack = None

  phenix.refine --show-defaults=all.help
you get:

      symmetry_operation = None
        .help = "The bond is between atom_1 and symmetry_operation * atom_2, "
                "with atom_1 and atom_2 given in fractional coordinates. "
                "Example: symmetry_operation = -x-1,-y,z"

The symmetry_operation must produce the fractional coordinates of
atom_2 exactly (within floating-point precision). I.e. depending on
where the atoms are, you may need -x+2,-y-3,z or similar.

Let me know if you need help figuring out the fractional coordinates.


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