[phenixbb] occupancy refinement of a metal ion

Pavel Afonine pafonine at lbl.gov
Wed Oct 20 11:10:10 PDT 2010

  Hi Christian,

> if I understood the manual correctly I could refine the occupancy and set the
> B-Factor to a constant value, or vice versa.

you can do both, or either one, in any combination and applied to any 
selected set of atoms. So, yes, your understanding is correct.

> Is there a possibility that
> phenix refine the B-Factor automatically to the value of the coordinating
> residues and adjust than the occupancy to a good value?

What you described should happen in practice, but since this is all done 
using restraints (and not constraints), the outcome can be approximate 
to what you expect (and cannot be promised for 100% sure). Indeed, the 
B-factors of coordinating residues (or any atoms close in space) are all 
restrained to be similar (using similarity restraints described here: 
http://www.phenix-online.org/newsletter/CCN_2010_07.pdf ; See article 
about ADP in phenix.refine.). The occupancies are refined too, if 
requested or if the initial values in input PDB file are between 0 and 
1. So I guess all you need to to set up approximately good/correct 
initial values for B-factors and occupancies, refine them all and see 
what happens. Since refinement of occupancies and B-factors is 
correlated setting different initial values may result in slightly 
different refinement results.

Let me know if you have any questions or need any help with this.


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