[phenixbb] Phenix.Refine: Missing High Resolution Data
Pavel Afonine
pafonine at lbl.gov
Wed Mar 14 10:50:05 PDT 2018
Hi Mark,
phenix.refine may remove a few reflection outliers as described in Read,
R. J. (1999). Acta Cryst. D55, 1759–1764. Conversion I to F may also
result in a loss of few reflections.
If you send me original sca file, mtz file and tell how you obtained mtz
file then I may be able to provide more diagnostics.
Pavel
On 3/14/18 10:47, Mark A. White wrote:
> Hello,
>
> I have several data sets which seem to loose completeness in their
> high-resolution shells when the HKL *.sca file is converted into an
> MTZ. I am using the recommended Diederichs CC1/2 cut off of 0.5,
> which is usually an I/s <2. I also have an usually high redundancy in
> these data sets, not sure if that has any effect. Here is a typical
> comparison of the Phenix statistics and the HKL values. Note that the
> resolution bins do not match, and that the Phenix refinement was
> truncated to 3.0Å.
>
> PHENIX HKL2000/Scalepack
> RESOLUTION RANGE COMPL total CC1/2 CC* Redn ScP-Angstrom
> 50.1353 - 8.8720 97 97.8 0.989 0.997 10.9 70.00 7.87
> 8.8720 - 7.0483 99 -
> 7.0483 - 6.1591 100 99.6 0.990 0.997 12.8 7.87 6.25
> 6.1591 - 5.5968 100 99.7 0.991 0.998 12.9 6.25 5.46
> 5.5968 - 5.1961 99 -
> 5.1961 - 4.8900 99 99.6 0.991 0.998 13.0 5.46 4.96
> 4.8900 - 4.6453 99 99.5 0.986 0.996 12.9 4.96 4.60
> 4.6453 - 4.4432 99 99.2 0.990 0.997 13.1 4.60 4.33
> 4.4432 - 4.2723 99 -
> 4.2723 - 4.1249 99 99.8 0.988 0.997 13.3 4.33 4.11
> 4.1249 - 3.9960 99 99.9 0.989 0.997 13.4 4.11 3.94
> 3.9960 - 3.8818 99 99.9 0.987 0.997 13.5 3.94 3.78
> 3.8818 - 3.7796 100 -
> 3.7796 - 3.6875 100 99.8 0.985 0.996 13.4 3.78 3.65
> 3.6875 - 3.6037 100 100.0 0.975 0.994 13.5 3.65 3.54
> 3.6037 - 3.5270 100 -
> 3.5270 - 3.4565 100 100.0 0.964 0.991 13.5 3.54 3.44
> 3.4565 - 3.3912 100 -
> 3.3912 - 3.3307 97 99.9 0.966 0.991 12.1 3.44 3.35
> 3.3307 - 3.2742 87 100.0 0.916 0.978 10.2 3.35 3.27
> 3.2742 - 3.2214 68 100.0 0.857 0.961 8.5 3.27 3.19
> 3.2214 - 3.1719 54 -
> 3.1719 - 3.1252 41 100.0 0.763 0.930 7.4 3.19 3.12
> 3.1252 - 3.0812 33 99.9 0.616 0.873 6.4 3.12 3.06
> 3.0812 - 3.0396 24 -
> 3.0396 - 3.0001 18 98.4 0.547 0.841 5.8 3.06 3.00
> 95.1 0.307 0.685 5.2 3.00 2.95
> 89.8 0.302 0.681 4.8 2.95 2.90
> 98.9 0.982 0.995 10.9 All reflect.
> --
> Yours sincerely,
>
> Mark A. White, Ph.D.
> Associate Professor of Biochemistry and Molecular Biology,
> Manager, Sealy Center for Structural Biology and Molecular Biophysics
> Macromolecular X-ray Laboratory,
> Basic Science Building, Room 6.658A
> University of Texas Medical Branch
> Galveston, TX 77555-0647
> Tel. (409) 747-4747
> mailto://[email protected]
> http://xray.utmb.edu
>
> QQ: "Don’t persist in folly. Some people commit themselves to their
> errors. They commit one error and consider it constancy to go on that
> way."
> - Baltasar Gracian (1658)
>
>
>
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