From b7a440bcbdf8a6d2da45f211252ea197c231644a Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Mon, 5 Oct 2026 16:34:59 +0200 Subject: [PATCH] Docs: verified DOIs for Wilson (1949) and Whittaker; centre-of-symmetry references Both DOIs were resolved against doi.org/Crossref (title, volume and pages match), so the "DOI not verified" notes go. The analysis reference's References list gains Wilson / Howells-Phillips-Rogers and Baur & Kassner, whose methods 13.1 now describes (CLAUDE.md: a method described there is listed there as well as in ACKNOWLEDGEMENT.md). Every other DOI in ACKNOWLEDGEMENT.md, the CPU_DATA_ANALYSIS* pages, the RUGNUX* pages, README.md and the battery README resolves. Co-Authored-By: Claude Opus 5.5 (1M context) Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB --- docs/ACKNOWLEDGEMENT.md | 7 ++++--- docs/CPU_DATA_ANALYSIS.md | 4 +++- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/docs/ACKNOWLEDGEMENT.md b/docs/ACKNOWLEDGEMENT.md index 1a76522e7..a71e7ceab 100644 --- a/docs/ACKNOWLEDGEMENT.md +++ b/docs/ACKNOWLEDGEMENT.md @@ -206,7 +206,8 @@ G. Winter, D. G. Waterman et al., "Robust background modelling in DIALS" (2016), centric intensity distributions of its resolution shell, with the symmetry enhancement factor, is Wilson's statistics; rejecting only observations that are also significant, and keeping a reflection whose observations are all large, follows AIMLESS's EMAX test. A. J. C. Wilson, "The probability -distribution of X-ray intensities" (1949), Acta Cryst. 2, 318-321 (DOI not verified, so omitted); +distribution of X-ray intensities" (1949), Acta Cryst. 2, 318-321 +[doi:10.1107/S0365110X49000813](https://doi.org/10.1107/S0365110X49000813); P. Evans, "Scaling and assessment of data quality" (2006), Acta Cryst. D62, 72-82 [doi:10.1107/S0907444905036693](https://doi.org/10.1107/S0907444905036693). @@ -260,8 +261,8 @@ P. A. Karplus, "Better models by discarding data?" (2013), Acta Cryst. D69, 1215 curve (a second-difference penalty, the smoothness chosen by cross-validation) in the form P. H. C. Eilers gave Whittaker's graduation: P. H. C. Eilers, "A perfect smoother" (2003), Anal. Chem. 75, 3631-3636 [doi:10.1021/ac034173t](https://doi.org/10.1021/ac034173t); E. T. Whittaker, -"On a new method of graduation" (1923), Proc. Edinburgh Math. Soc. 41, 63-75 (DOI not verified, so -not given). +"On a new method of graduation" (1923), Proc. Edinburgh Math. Soc. 41, 63-75 +[doi:10.1017/S0013091500077853](https://doi.org/10.1017/S0013091500077853). **Fisher's z-transformation** — the cross-validation of the scaling correction surfaces averages the change of the half-set CC1/2 over resolution shells on atanh(CC), so that the shells near CC = 1, where diff --git a/docs/CPU_DATA_ANALYSIS.md b/docs/CPU_DATA_ANALYSIS.md index 75c50a323..bfb7de4f6 100644 --- a/docs/CPU_DATA_ANALYSIS.md +++ b/docs/CPU_DATA_ANALYSIS.md @@ -14,7 +14,7 @@ This document describes the crystallographic algorithms implemented in Jungfrauj 8. Bragg integration by either 2D box summation or profile fitting (Kabsch, reference-free), 9. scaling and merging, 10. merge-level error modelling, outlier rejection and the resolution cutoff, -11. space-group determination from the merged intensities (Laue group, screw axes, glide planes, centering), the twinning check and the translational pseudo-symmetry check, +11. space-group determination from the merged intensities (Laue group, screw axes, glide planes, centering, the centre of symmetry), the twinning check and the translational pseudo-symmetry check, 12. auxiliary statistics (Wilson plot, ⟨I/σ(I)⟩, CC1/2, CCref), 13. amplitude estimation (French–Wilson) and R-free test-set flagging, 14. optional model-based validation: rigid-body placement of a supplied model, R-free against it, sigma_A-weighted 2mFo−DFc / mFo−DFc electron-density maps, and an anomalous difference map with the strongest anomalous sites named. @@ -47,6 +47,8 @@ The methods draw on, and in places reimplement, solutions from: - P. Gasparotto, L. Barba, H.-C. Stadler et al., "TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography", *J. Appl. Cryst.* **57** (2024), 931-944 (the algorithm of the `ffbidx` fast-feedback indexer, §4). - I. Křivý & B. Gruber, "A unified algorithm for determining the reduced (Niggli) cell", *Acta Cryst.* **A32** (1976), 297-298, and International Tables for Crystallography Vol. A, Table 9.2.5.1 (the Niggli reduction and the lattice-character table of §5.3/§6). - J. E. Padilla & T. O. Yeates, "A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning", *Acta Cryst.* **D59** (2003), 1124-1130 (the L test, §13.2). +- A. J. C. Wilson, "The probability distribution of X-ray intensities", *Acta Cryst.* **2** (1949), 318-321, and E. R. Howells, D. C. Phillips & D. Rogers, "The probability distribution of X-ray intensities. II. Experimental investigation and the X-ray detection of centres of symmetry", *Acta Cryst.* **3** (1950), 210-214 (the acentric and centric intensity distributions behind the centre-of-symmetry statistics of §13.1 and the Wilson outlier test of §13.3). +- W. H. Baur & D. Kassner, "The perils of Cc: comparing the frequencies of falsely assigned space groups with their general population", *Acta Cryst.* **B48** (1992), 356-369 (writing the centrosymmetric group where the absences cannot decide the centre, §13.1). - R. J. Read, P. D. Adams & A. J. McCoy, "Intensity statistics in the presence of translational noncrystallographic symmetry", *Acta Cryst.* **D69** (2013), 176-183 (the native-Patterson detection of translational pseudo-symmetry, and the intensity modulation it produces, which the axial-zone screw-absence test scores against). - A. Barty, R. A. Kirian, F. R. N. C. Maia et al., "Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data", *J. Appl. Cryst.* **47** (2014), 1118-1131 (peakfinder8: the per-resolution-ring background statistics of §3.2). - A. Hennequin, B. Couturier, V. V. Gligorov & L. Lacassagne, "SparseCCL: Connected Components Labeling and Analysis for sparse images", DASIP 2019, 65-70 (the connected-component labelling of §3.4, used via ACTS/traccc).