[phenixbb] occupancy refinement

Christian Roth christian.roth at bbz.uni-leipzig.de
Wed Jan 27 01:59:11 PST 2010

Dear all, 

I refine a structure of a protein to 1.4 A and found a few SO4-Ions.  I tried 
to refine this sulfurs and some of these seems to be not fully occupied, as the 
negative difference density suggest. I tried to refine the occupancy of the 
sulfate ions to get an idea how strong the different binding sites might be 
occupied. All sulfate ions are in Chain C of my pdb. I tried to refine the 
occupancy individually using refine.occupancy.individual SO4 but this lead to 
different occupnacies for every atom for every atom and theix cant be the case 
for sure.  Then I tried and group occupancy  with resname=SO4 but now every 
sulfate ion has the same occupancy, which is indicated from my previous 
refinements  also not the case, because two ions have no negative difference 
density. At the momentI can not figure out how I should combine the keywords 
for the individual occupancy refinement of the different sulfate ions. In my 
structure. Should I define for every ion a different chain or how I could 
overcome this problem?
I would be very happy if anyone has a idea to sove this problem or tell me 
what keyword I misunderstood in the documentation.

Best regards 


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