[phenixbb] occupancy_sum_constraints

Pavel Afonine pafonine at lbl.gov
Wed Jul 15 15:42:11 PDT 2020

Hi Petros,

I believe this question is addressed here:

13 typical occupancy refinement scenarios and available options 
<http://phenix-online.org/newsletter/CCN_2015_07.pdf#page=12>— Afonine, 
P.V. (2015)./Comput. Crystallogr. Newsl./*5*, 37-46.


Please feel free to come back with more questions, if needed!


> Dear all,
> I have a metal compound interacting with a protein and I am facing the 
> following problem.
> Initially, the metal is equatorially complexed with chlorides, which 
> are progressively exchanged by water molecules. This hydrolysis is 
> clear from our spectroscopic analysis, but also from the anomalous 
> maps, which show weaker peaks for the most exposed chlorides.
> The question regarding phenix.refine is:
> How can I refine the occupancies of the alternative species (chlorides 
> and water molecules) and to constrain their sum into the occupancy of 
> the metal, which is also under refinement?
> I cannot find the proper selection syntax to deal with this situation.
> Can you help me on that?
> Thank you in advance.
> Petros
> P.S. I remember I could treat this kind of problem with shelxl but it 
> has been a lot of time since I last used shelxl for high resolution 
> protein refinement and I would not like to go back.

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