[phenixbb] Phenix.Refine: Missing High Resolution Data

A. Radu Aricescu radu at strubi.ox.ac.uk
Wed Mar 14 11:19:33 PDT 2018


Hi Mark,

I noticed this in the past, I think it is an HKL2000 merging issue, not related to Phenix. I would try to output scaled but unmerged data from HKL2000 (tick "No Merge Original Index", and do not use auto corrections), and do the merging in Aimless. Then feed the output mtz to Phenix. I bet completeness will be OK.

However, I am very curious if Pavel finds an alternative solution. 

Related to Mark's resolution bin point: Pavel, is there a way to specify the resolution bins Phenix uses?  For example asking for an equal number of reflections to be present in each bin? Stats get bad (and probably meaningless) when outer bins are cut very thin and contain a tiny number of reflections.... a particular problem with anisotropic datasets....

Best wishes,

Radu


------------------------------------------
A. Radu Aricescu, PhD
Professor of Molecular Neuroscience
MRC Senior Research Fellow

University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive, Oxford OX3 7BN
United Kingdom
Phone: +44-1865-287564
Fax: +44-1865-287547
https://www.strubi.ox.ac.uk/research/a-radu-aricescu


---- Original message ----
>Date: Wed, 14 Mar 2018 12:47:06 -0500
>From: phenixbb-bounces at phenix-online.org (on behalf of "Mark A. White" <mawhite at utmb.edu>)
>Subject: [phenixbb] Phenix.Refine: Missing High Resolution Data  
>To: PHENIX BB <phenixbb at phenix-online.org>
>
>   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
>   3.0AA.
>
>     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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