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 viewpoint... 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 multiplicity_of_the_special_position ------------------------------------ multiplicity_of_the_general_position 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: http://www.wwpdb.org/documentation/format32/sect9.html This leaves me uncertain. Then: http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Items/_atom_site.occupancy.h... 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? Ralf