[phenixbb] PHENIX user mailing list (Ca2+ ion in a special position)

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Sun Mar 29 15:30:43 PDT 2009

> Ralf W. Grosse-Kunstleve wrote:
> > phenix.refine uses the correct symmetry factor automatically
> > (internally). Unless you have an actual partial occupancy, the
> > occupancy factor in the pdb file should be 1, irrespective of the
> > multiplicity of the special position.
> > 
> Doesn't that violate the mandate that the pdb file represent the
> contents of the  AU?
> Unless I misunderstand Maia's structure, the Ca++ is shared
> between two asymmetric units, so each AU contains 0.5 of it?

That's the first time for me to look at the situation from that

My thinking so far:

  Given the space group symmetry, the special-position information
  is in the coordinates. From that follows directly the multiplicity
  of the Wyckoff position, as listed in the International Tables. If
  the occupancy factor is convoluted with the


  quotient, the result is not an occupancy factor anymore since two
  distinct concepts are mixed.

But ultimately, what should be in the PDB occupancy column is a matter
of convention.

Prompted by your message I looked at:


This leaves me uncertain.


Which says:

  The fraction of the atom type present at this site.
  The sum of the occupancies of all the atom types at this site
  may not significantly exceed 1.0 unless it is a dummy site.

There is no mention of including the symmetry correction.

Is anyone aware of other resources that define what to do about
the symmetry correction factor for atoms on special positions?


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