[phenixbb] R-factor difference between phenix and sftools

[Pavel Afonine]

Thanks Tim, yes missed this one!

Hi Simon,

the differences in R-factors you observe are most likely because we use 
improved bulk-solvent modeling and overall scaling procedure. This is 
described here:

Bulk-solvent and overall scaling revisited: faster calculations, 
improved results.
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 
expectable.

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).

Pavel


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,
> Tim
>
> On 10/12/2014 08:25 PM, Simon Jenni wrote:
>> Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors
>> are:
>>
>>     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" \
>>     unmerged_data="xscale.hkl"
>>
>>     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
>>     Y
>>     select col R_FREE_FLAGS > 0
>>     correl col FOBS FMODEL
>>     select invert
>>     correl col FOBS FMODEL
>>     quit
>>     Y
>>     eof
>>
>>     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.
>>
>>
>>
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>>
>
>
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