[phenixbb] R-factor difference between phenix and sftools

Tim Gruene tg at shelx.uni-ac.gwdg.de
Mon Oct 13 11:25:43 PDT 2014


Hi Pavel,

thanks for the explanation. Call me lazy as I have not read the
reference yet - does it explain how the bulk-solvent is incorporated
into the model so that it is not represented in FMODEL written by Phenix
(see Simon's script for sftools)? My naive thinking is that the bulk
solvent model add to FMODEL so that particularly the calculated low
resolution reflections match better the measured ones.

Best,
Tim

On 10/13/2014 08:21 PM, Pavel Afonine wrote:
> 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.
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
>>
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>> phenixbb at phenix-online.org
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> 
> 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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