[phenixbb] FreeR set reduced by half in twin crystal refinement?
krahn at niehs.nih.gov
Wed Oct 7 09:03:08 PDT 2009
> Hi everyone,
> I have a P31 twin crystal, resolution 2.0, and with twin fraction 0.451.
> I use phenix.refine to refine the structure and with freeR set to 8%.
> % phenix.refine data.sca model.pdb twin_law="h,-h-k,-l" xray_data.r_free_flags.generate=True xray_data.r_free_flags.fraction=0.08
> Final: r_work = 0.1793 r_free = 0.2258 bonds = 0.011 angles = 1.557
> After the refinement, it seems like my freeR set size reduced by half
> (3.67%). Is it due to the twin effect, or something is wrong with my
> And if I use ccp4 program “scalpeak2mtz “ to convert the .sca to .mtz
> and with freeR fraction set to 8%. Then refine it with phenix.
> % phenix.refine data.mtz model.pdb twin_law="h,-h-k,-l"
> Final: r_work = 0.1669 r_free = 0.1970 bonds = 0.010 angles = 1.406
> It turns out, my test set is still 8%, and R/Rfree looks even better
> than the first one. So I am wondering which one is the correct one and why?
My first guess is that the R-free set generated in CCP4 is not set to
follow twin laws, so you have work and free reflections associated by
twinning. However, I would expect PHENIX to check this.
As for the reduced size, that probably comes from the way the twinned
test set is calculated. Maybe it is a bug. Are you using anomalous data?
What is the PHENIX version?
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