[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://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)
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20180314/dbe2499a/attachment.htm>


More information about the phenixbb mailing list