Hi,

a free set in phenix.refine is choosen such that

- you have at least n% of free flags, but not more then 2000+epsilon (typically)
- it follows any possible twin law (not user specified, it follows symmetry of the lattice)

the ccp4 suite doesn't follow the same rules, so you will
- have more free flags
- have twin related reflections in your mixed between the test and work set. This reduces the rfree greatly and should be avoided.

P




2009/10/7 lauren <lauren@gate.sinica.edu.tw>

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

REMARK   3   FREE R VALUE                     : 0.2258

REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 3.67

REMARK   3   FREE R VALUE TEST SET COUNT      : 2013

 

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

REMARK   3   FREE R VALUE                     : 0.2022

REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 7.80

REMARK   3   FREE R VALUE TEST SET COUNT      : 4326

 

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

 


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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
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