[phenixbb] phenix.refine change: support for residues on symmetry elements

[Ralf W. Grosse-Kunstleve]

The current development version of phenix.refine (dev-268 or later)
supports residues located on symmetry elements, e.g. SO4 on a three-fold
axis. phenix.refine now computes structure factors slightly differently
compared to older versions.
The new rules are:

- Atoms with occupancy == 1 are subject to automatic handling of the
  symmetry.
  Example:
    An atom near a three-fold axis (distance to symmetry copy <= 0.5 A)
    is moved onto the axis and constrained in refinement to stay on
    the axis. The "special position factor" (1/3 is this case) is taken
    into account internally. The factor does not appear in the occupancy.

- Atoms with occupancy != 1 are assumed to take the special position
  factor into account in the occupancy. Automatic handling of the
  symmetry is turned off.
  Example:
    A disordered SO4 molecule near a three-fold axis should have
    occupancies of 0.33 for all atoms.

- If all atoms in a residue have occupancies != 1, all
  nonbonded symmetry interactions between the atoms in the
  residue are disabled.

These three rules are meant
  - to bring phenix.refine in line with other programs and the PDB.
  - "to do the right thing" in most cases without manual intervention.

Please let me know if you see problems with the new way phenix.refine
uses occupancies to determine special position constraints and
exclusions for nonbonded symmetry interactions.

Does anyone need atoms with partial occupancies but constrained to
stay on a symmetry axis during refinement?

Ralf