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

Dale Tronrud det102 at uoxray.uoregon.edu
Mon Mar 30 16:01:46 PDT 2009

"It depends on what the meaning of the word IS is"

   Here it depends on the meaning of the word "site".  Every program
I can recall, except for phenix.refine, has operated with the
convention that every atom in the model is subject to symmetry
expansion by all the equivalent positions.  This convention has
the result that an atom on a special position doubles (or triples,
or ...) up and its occupancy has to be reduced to get the electron
density right.  (Obviously no one applies the same convention to
electron density.  Consistency is not a hallmark of humanity)

   I'm not saying that one way or the other is "right".  I think
its pretty clear that the traditional convention was created for
the convenience of the programmer and many users have mistakenly
left the occupancy at 1 with the result of inflated B factors.
Your convention does not require that the user recognize or even
understand special positions which is consistent with your goals of

   The only problem, as usual, is interoperability.  When one
takes a phenix.refine model into Refmac or Shelxl the occupancy
will be too high and this will surprise the users.

   Since interoperability is the wwPDB's business they should
clarify what is expected to be in a PDB file.  If it comes down to
a vote based on what's already in the PDB, I think you'll lose.

Dale Tronrud

Ralf W. Grosse-Kunstleve wrote:
>> 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.html
> 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
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