[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://[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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