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Maia Cherney chern at ualberta.ca
Sun Mar 29 13:03:11 PDT 2009

Thank you, Ralf and Nick for your help.
I could see from the lof file that phenix.refine determined 2 sites at 
special positions, but I thought it did nothing about it, as the 
occupancies were brought back to 1. Thank you for your explanation that 
phenix.refine actually takes this into account.


Ralf W. Grosse-Kunstleve wrote:
> Hi Maia,
>> I have  a Ca2+ ion in a special position. the ocupancy should be 0.5, as
>> the other half belongs to a symmetry-related molecule. However,
>> refinement makes the occupansy 1. What should I do to prevent this?
>> Should not it find automatically that?
> 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.
> Let me know if this doesn't answer your question.
> Ralf
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