[phenixbb] R-factor difference between phenix and sftools

Pavel Afonine pafonine at lbl.gov
Mon Oct 13 11:37:52 PDT 2014


Hi Tim,

oh, I see..

Yes, you are right, FMODEL contains everything, including bulk-solvent.

Any MTZ file out of phenix.refine contains four blocks of data:
1) input reflections (Fobs or Iobs, flags);
2) data actually used in refinement. For example, if Iobs were input, 
phenix.refine will convert them into Fobs and use in refinement. That's 
what will be in this block.
3) Fmodel (the total model structure factors including all scales, 
bulk-solvent etc);
4) various Fourier map coefficients.

Using 2) and 3) you can reproduce reported R-factors exactly. Basically 
you can read such MTZ file with a script of your choice, take 
corresponding arrays and employ R-factor formula from a text book, and 
you will obtain reported R-factors.

Now, I'm not a great expert in sftools so I can't really comment on the 
script that Simon quoted below.. If it really does take arrays of data 
from 2) and 3) and uses R-factor formula then the numbers must match... 
Otherwise this is puzzling!

Simon, if you send me MTZ file offlist I will have a closer look.. - thanks!

All the best,
Pavel


On 10/13/14 11:25 AM, Tim Gruene wrote:
> 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.
>>>>
>>>>
>>>>
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>>>>
>>>
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>>



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