[phenixbb] FreeR set reduced by half in twin crystal refinement?

Joe Krahn krahn at niehs.nih.gov
Wed Oct 7 09:03:08 PDT 2009

lauren wrote:
> 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 
> Result:
> 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 
> refinement?
> 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?
> Thanks!
> Lauren

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?

Joe Krahn

More information about the phenixbb mailing list