[phenixbb] Phenix.Refine: Missing High Resolution Data

Jeffrey, Philip D. pjeffrey at princeton.edu
Thu Mar 15 12:30:07 PDT 2018


Mark

Suggest MTZDUMP the intermediate .mtz file - I assume you're using SCALEPACK2MTZ to convert .sca, and if not this would be useful for debug - to see which program the completeness vs resolution table agrees with.

This may be a Scalepack "feature" where I've infrequently noticed something like: the resolution of the reflections may be calculated from unit cell dimensions before post-refinement (e.g. the first .x file) which then causes a high resolution cutoff mismatch when the post-refined unit cell is used for calculations downstream of Scalepack.

Phil Jeffrey
Princeton
________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Mark A. White [mawhite at utmb.edu]
Sent: Wednesday, March 14, 2018 1:47 PM
To: PHENIX BB
Subject: [phenixbb] Phenix.Refine: Missing High Resolution Data

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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