[phenixbb] R factor

zhangh1 at umbc.edu zhangh1 at umbc.edu
Sun Sep 19 01:17:11 PDT 2010


Hi Pavel:

Never mind. The data.mtz is missing about 10% reflections, without which
the Fc map (by model_vs_data --map=fc) looks weird (showing some big
density like heavy metal not in the model). Thats why I wondered whether
model_vs_data --map=fc involved something else.

Just curious, why missing 10% reflections generated "heavy-metal" like
density in solvent region? And in this case, is that more reasonable to
manally adding the missing reflection by setting Fo=Fc?

Best Regards, Hailiang

> Hi Pavel:
>
> Just want to make sure, by doing:
>
> *********
> phenix.model_vs_data model.pdb data.mtz --map=fc
> *********
>
> will 0Fobs+Fmodel/P0Fobs+Fmodel in the output mtz file
> (fo_0Fobs+Fmodel_map_coeffs.mtz) be the calculated results from model.pdb,
> which is independent (eg NO sigmaa weighting) from the experemental Fo in
> data.mtz?
>
> Thanks!
>
> Best Regards, Hailiang
>
>
>>   Hi Hailiang,
>>
>>> I want to calculate Fc based on the PDB file and reproduce the R factor
>>> in
>>> it.
>>
>> then phenix.model_vs_data is the right tool to accomplish this.
>>
>>> I first tried phenix.model_vs_data. It optimized ksol bsol and b_cart,
>>> and the output R factor (0.2143) is close enough to that in PDB
>>> (0.215).
>>
>> The difference between the R-factors is very small. See
>>
>> J. Appl. Cryst. (2010). 43, 669-676.
>> 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
>> and P. D. Adams
>>
>> for explanations of possible differences between published and
>> re-computed R-factors.
>>
>>> However, it didn't generate mtz files containing the calculated Fc.
>>
>> Yes, it's not supped to do that. Actually, phenix.model_vs_data can
>> output the map defined as:
>>
>> [p][m]Fo+[q][D]Fc[kick][filled].
>>
>> Examples: 2mFo-DFc, 3.2Fo-2.3Fc, Fc, anom, fo-fc_kick.
>>
>> So, if you say
>>
>> phenix.model_vs_data model.pdb data.mtz --map=fc
>>
>> you will get an MTZ file with desired structure factors. So, yes, you
>> can get what you want out of phenix.model_vs_data !
>>
>>> Then, I take the optimized ksol bsol and b_cart as the input and tried
>>> phenix.fmodel.
>>
>> This should (to some accuracy) reproduce the R-factor reported by
>> phenix.model_vs_data.
>>
>>> I wrote my own code to calcuate the R factor. However, I
>>> got a lower R factor (0.2078).
>>
>> Any bugs ?
>>
>>> I think the reason might be my R calculation formula
>>> (sigma(fo-fc)/sigma(fo)) is wrong; or model_vs_data did more than just
>>> did
>>> flat solvent correction and anisotropic scaling.
>>
>> Yup, you are missing the scale factor (unless you applied it to your fc
>> already). See previous email for details - the script there shows the
>> R-factor formula.
>>
>> Good luck!
>> Pavel.
>>
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>





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