[phenixbb] Using LigandFit to identify unknown density

Peter Zwart phzwart at gmail.com
Wed Jan 27 14:06:23 PST 2010

Hi Maia,

I think the B values of your ligand have restraints on them
encouraging them to be similar to surrounding atoms. This additional
info reduces the dependence between occupancy and B value.



2010/1/27 Maia Cherney <chern at ualberta.ca>:
> Hi Pavel,
> I have six ligands at partial occupacies in my structure. Simultaneous
> refinement of occupancy and B factors in phenix gives a value of 0.7 for the
> ligand occupancy that looks reasonable.
> How does phenix can perform such a refinement given the occupancies and B
> factors are highly correlated? Indeed, you can increase/decrease the ligand
> occupancies while simultaneously increacing/decreasing their B factors
> without changing the R factor value. What criteria does phenix use in such a
> refinement if R factor does not tell much?
> Maia
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
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PHENIX: http://www.phenix-online.org
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