[phenixbb] FreeR set reduced by half in twin crystal refinement?
Peter Zwart
phzwart at gmail.com
Wed Oct 7 12:43:33 PDT 2009
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 at 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
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
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