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: [email protected] (on behalf of "Mark A. White" ) Subject: [phenixbb] Phenix.Refine: Missing High Resolution Data To: PHENIX BB

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) ________________ _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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: [email protected] [[email protected]] on behalf of Mark A. White [[email protected]] 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://[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)