[phenixbb] Phenix.Refine: Missing High Resolution Data

Mark A. White mawhite at utmb.edu
Wed Mar 14 10:47:06 PDT 2018


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://mawhite@utmb.edu 
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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