[phenixbb] occupancy refinement

Marco Bellinzoni marco.bellinzoni at pasteur.fr
Wed Jan 27 01:14:43 PST 2010

Hi Christian,

all you have to do is to define each sulfate as a constrained group for 
occupancy refinement, like this:

constrained_group {
        selection = "chain C and resid x"
      constrained_group {
        selection = "chain C and resid y"

where resid is simply the residue number. The occupancy of all atoms 
that belong to the same constrained group will be refined to the same value.

Best wishes,

Christian Roth wrote:
> 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 
> Christian
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Marco Bellinzoni
Unité de Biochimie Structurale
Institut Pasteur
25, rue du Dr. Roux
75724 Paris Cedex 15
Tel. +33 (0)1 45688608
Fax. +33 (0)1 45688604

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