[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.
HTH
P
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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
--
-----------------------------------------------------------------
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
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
-----------------------------------------------------------------
More information about the phenixbb
mailing list