[phenixbb] R-factor difference between phenix and sftools
pafonine at lbl.gov
Mon Oct 13 11:21:46 PDT 2014
Thanks Tim, yes missed this one!
the differences in R-factors you observe are most likely because we use
improved bulk-solvent modeling and overall scaling procedure. This is
Bulk-solvent and overall scaling revisited: faster calculations,
Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A. Acta Cryst.
D69, 625-34 (2013).
Specifically, Figures 3-4 in this paper make your observations very
Other contributions to differences are discussed here:
phenix.model_vs_data: a high-level tool for the calculation of
crystallographic model and data statistics.
P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W.
Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart,
P.D. Adams J. Appl. Cryst. 43, 677-685 (2010).
On 10/13/14 11:10 AM, Tim Gruene wrote:
> Dear Simon,
> I found this a very puzzling observation and given the high throughput
> of this board, it is likewise puzzling you have not received a reply yet
> - or have you?
> Best regards,
> On 10/12/2014 08:25 PM, Simon Jenni wrote:
>> Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors
>> Final R-work = 0.3221, R-free = 0.3638
>> phenix.cc_star agrees:
>> phenix.cc_star com_001.pdb com_001.mtz \
>> f_obs_labels="F-obs,SIGF-obs" \
>> f_model_labels="F-model,PHIF-model" \
>> r_work: 0.322
>> r_free: 0.364
>> so does phenix.model_vs_data:
>> phenix.model_vs_data com_001.pdb com_001.mtz
>> r_work : 0.3221
>> r_free : 0.3638
>> sigma_cutoff : None
>> However, when I calculate the R-factors with sftools, I get a discrepancy
>> between the phenix and sftools results:
>> sftools << eof
>> read com_001_f_model.mtz
>> select col R_FREE_FLAGS > 0
>> correl col FOBS FMODEL
>> select invert
>> correl col FOBS FMODEL
>> R-work: 33.6
>> R-free: 38.1
>> Does anyone perhaps know what causes this difference?
>> With best regards, Simon
>> PS: The structure is in spacegroup P212121 with strong pseudocentering tNCS
>> (dimer in the asymmetric unit, native Patterson peak at 0.500 0.500 0.497).
>> No indication for a P21 twin (L-test and refinement in P21 with twin law),
>> not higher symmetry spacegroup I222 (alternating strong and weak
>> reflections are visible in the diffraction patterns, resolved structural
>> differences in the two protomers of the dimer). Two datasets from different
>> beamlines. As might be expected, the R-factors after refinement are
>> unusually high (e.g. 28/35 [conventional resolution cutoff at 3.1 A], 32/36
>> with Kay's CC cufoff at 2.6 A). I wanted to compare refinements between
>> different programs to see how they cope with the unexpected bimodal
>> amplitude distribution.
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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> phenixbb at phenix-online.org
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