[phenixbb] occupancy refinement of a metal ion
pafonine at lbl.gov
Wed Oct 20 11:10:10 PDT 2010
> 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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