Jungfraujoch/docs/ACKNOWLEDGEMENT.md

Acknowledgements

Citation: F. Leonarski, M. Bruckner, C. Lopez-Cuenca, A. Mozzanica, H.-C. Stadler, Z. Matej, A. Castellane, B. Mesnet, J. Wojdyla, B. Schmitt and M. Wang, "Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors" (2023), J. Synchrotron Rad., 30, 227-234 doi:10.1107/S1600577522010268.

Funding and support

The project is supported by:

• Innosuisse via Innovation Project "NextGenDCU high data rate acquisition system for X-ray detectors in structural biology applications" (101.535.1 IP-ENG; Apr 2023 - Sep 2025).
• ETH Domain via Open Research Data Contribute project (Jan - Dec 2023).
• AMD University Program with donation of licenses of Ethernet IP cores and Vivado software.

Automatic processing as an expert system

Global Phasing Ltd — rugnux owes two of its guiding ideas to Gérard Bricogne and his colleagues at Global Phasing: the Fourier-transform indexing its de-novo indexers descend from, which Bricogne proposed in 1986 (see Indexing below), and the view of data processing as an expert system, embodied in their autoPROC, which is the model rugnux aims at.

autoPROC — rugnux's goal is a fully automatic pipeline that takes the decisions an experienced crystallographer would take while processing a dataset, and reports each decision together with the evidence it rests on, so that a bare invocation gives the best answer available. autoPROC is the model and the target for that behaviour. The reasons rugnux gives for a weak stretch of a sweep also use autoPROC's wording ("loss of centring during crystal rotation"). C. Vonrhein, C. Flensburg, P. Keller, A. Sharff, O. Smart, W. Paciorek, T. Womack and G. Bricogne, "Data processing and analysis with the autoPROC toolbox" (2011), Acta Cryst. D67, 293-302 doi:10.1107/S0907444911007773.

Crystallographic methods adopted from other packages

The analysis pipeline reimplements methods first published, and in most cases first implemented, by other crystallographic software. The code below is Jungfraujoch's own; the methods are theirs, and are acknowledged here. Where a package's source was consulted this is said explicitly. Most of these packages are neither linked nor vendored; the three that are - GEMMI, traccc and fast-feedback-indexer - also carry a licence obligation, recorded in THIRD_PARTY_NOTICES.md.

Spot finding

CrystFEL — spot finding, the three-ring integration region, the serial/stills processing model, and the per-frame indexing acceptance test (indexing_peak_check() in peaks.c). T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman, "CrystFEL: a software suite for snapshot serial crystallography" (2012), J. Appl. Cryst. 45, 335-341 doi:10.1107/S0021889812002312. The self-calibrating spot finder's per-resolution-ring background statistics, with the Bragg peaks excluded by iterated clipping, follow Cheetah's peakfinder8: A. Barty, R. A. Kirian, F. R. N. C. Maia, M. Hantke, C. H. Yoon, T. A. White and H. N. Chapman, "Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data" (2014), J. Appl. Cryst. 47, 1118-1131 doi:10.1107/S1600576714007626.

Spot extraction groups strong pixels into spots with the sparse connected-component labelling of the ACTS traccc project: P. Gessinger, H. M. Gray, A. Krasznahorkay, C. Leggett, J. Niermann, A. Salzburger, S. N. Swatman and B. Yeo, "traccc: GPU track reconstruction library for HEP experiments" (2025), arXiv:2505.22822; traccc. The CPU spot extractor adapts its SparseCCL source, and the CUDA spot extractor follows the design of its GPU counterpart - a backward-neighbour graph over a sorted hit list, resolved by a parallel union-find. traccc is MPL-2.0; see THIRD_PARTY_NOTICES.md. The SparseCCL algorithm itself is A. Hennequin, B. Couturier, V. V. Gligorov and L. Lacassagne, "SparseCCL: Connected Components Labeling and Analysis for sparse images" (2019), DASIP 2019, 65-70 doi:10.1109/DASIP48288.2019.9049184.

Indexing

Fourier-transform indexing — indexing a diffraction pattern, with no prior knowledge of the cell, by Fourier-transforming the reciprocal-space positions of its spots was proposed by Gérard Bricogne as a three-dimensional transform; the de-novo FFT indexers (-X fft, -X fftw) use the one-dimensional projection form of that idea described in the next paragraph. G. Bricogne (1986), in Proceedings of the EEC Cooperative Workshop on Position-Sensitive Detector Software (Phase III), LURE, Paris, p. 28 (a workshop proceedings without a DOI).

MOSFLM — the Rossmann FFT autoindexing algorithm and post-refinement practice, including which parameters are safe to refine per image and which must be refined over a wedge. The autoindexing algorithm itself — projecting the reciprocal-space points onto many directions and Fourier-transforming the 1D projection histograms — is I. Steller, R. Bolotovsky and M. G. Rossmann, "An algorithm for automatic indexing of oscillation images using Fourier analysis" (1997), J. Appl. Cryst. 30, 1036-1040 doi:10.1107/S0021889897008777; MOSFLM is the implementation whose practice is followed, described in H. R. Powell, "The Rossmann Fourier autoindexing algorithm in MOSFLM" (1999), Acta Cryst. D55, 1690-1695 doi:10.1107/S0907444999009506. A. G. W. Leslie and H. R. Powell, "Processing diffraction data with MOSFLM" (2007), in Evolving Methods for Macromolecular Crystallography, NATO Science Series II, vol. 245, 41-51 doi:10.1007/978-1-4020-6316-9_4; T. G. G. Battye, L. Kontogiannis, O. Johnson, H. R. Powell and A. G. W. Leslie, "iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM" (2011), Acta Cryst. D67, 271-281 doi:10.1107/S0907444910048675; H. R. Powell, T. G. G. Battye, L. Kontogiannis, O. Johnson and A. G. W. Leslie, "Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm" (2017), Nat. Protoc. 12, 1310-1325 doi:10.1038/nprot.2017.037.

fast-feedback-indexer — the known-cell indexer for serial stills (-X ffbidx) is PSI's fast-feedback-indexer library, linked at build time (BSD-3-Clause; see THIRD_PARTY_NOTICES.md), which implements the TORO algorithm: P. Gasparotto, L. Barba, H.-C. Stadler, G. Assmann, H. Mendonça, A. W. Ashton, M. Janousch, F. Leonarski and B. Béjar, "TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography" (2024), J. Appl. Cryst. 57, 931-944 doi:10.1107/S1600576724003182.

Cell reduction and lattice symmetry

GEMMI — symmetry operations, unit-cell and structure-factor machinery, and MTZ / XDS_ASCII I/O. Vendored in gemmi_gph/, so it also carries a licence obligation. M. Wojdyr, "GEMMI: A library for structural biology" (2022), J. Open Source Softw. 7, 4200 doi:10.21105/joss.04200.

Křivý & Gruber's Niggli reduction, and the lattice-character table — the reduction that puts every candidate cell in a comparable form is I. Křivý and B. Gruber, "A unified algorithm for determining the reduced (Niggli) cell" (1976), Acta Cryst. A32, 297-298 doi:10.1107/S0567739476000636, used through GEMMI's implementation; the table of lattice characters that maps a reduced cell to Bravais lattices and centrings follows International Tables for Crystallography Vol. A, Table 9.2.5.1.

Grosse-Kunstleve, Sauter & Adams's numerically stable cell reduction - the magnitude-scaled tolerance that decides the sign of a structurally-zero scalar product, and with it the Niggli type a reduced cell is presented in. R. W. Grosse-Kunstleve, N. K. Sauter and P. D. Adams, "Numerically stable algorithms for the computation of reduced unit cells" (2004), Acta Cryst. A60, 1-6 doi:10.1107/S010876730302186X.

Le Page's metric-symmetry search - the obliquity of each of the 81 candidate two-folds of a reduced cell, which is what tells a run that its lattice metric hosts more rotational symmetry than the group its intensities supported, and the derivation of the conventional axes from that rotation group, which is what the run then offers to the space-group search as a second lattice candidate. The two-fold search is used through GEMMI's implementation of it. Y. Le Page, "The derivation of the axes of the conventional unit cell from the dimensions of the Buerger-reduced cell" (1982), J. Appl. Cryst. 15, 255-259 doi:10.1107/S0021889882011959.

Integration and rotation geometry

XDS — rotation geometry and notation, the reciprocal Lorentz and partiality treatment, the maximum-likelihood mosaicity estimate, the MINPK criterion for rejecting a reflection whose predicted profile is not cleanly its own, the intensity-based test for a centred lattice, the recognition of shaded detector regions by comparing a pixel's background against the background at its own resolution (DEFPIX), and the scaling correction surfaces indexed by image number and detector region. W. Kabsch, "XDS" (2010), Acta Cryst. D66, 125-132 doi:10.1107/S0907444909047337; W. Kabsch, "Integration, scaling, space-group assignment and post-refinement" (2010), Acta Cryst. D66, 133-144 doi:10.1107/S0907444909047374.

Profile fitting with reweighted, de-biased variances is the Kabsch/Otwinowski iteration, from the second XDS paper above and from Z. Otwinowski and W. Minor, "Processing of X-ray diffraction data collected in oscillation mode" (1997), Methods Enzymol. 276, 307-326 doi:10.1016/S0076-6879(97)76066-X.

The two-dimensional integration architecture — integrating each image in the detector plane and only afterwards assembling a reflection's partials into a full across images, as against three-dimensional profile fitting through the image stack — is the architecture of DENZO/SCALEPACK and MOSFLM, and it is the one Rugnux's rotation pipeline follows (per-image profile-fitted integration, then partials combined into fulls; §9 and §10.6 of the data-analysis reference). The Otwinowski & Minor citation above and the MOSFLM citations below carry the credit for the paradigm as well as for the specifics taken from each.

Space group, twinning and pseudo-symmetry

POINTLESS (CCP4) — the space-group search. Stage A scores each candidate rotation operator by the correlation of I(h) with I(Rh) on resolution-normalised intensities (E²), as POINTLESS does — both arms of a symmetry pair sit at the same |s|, so on raw intensities the resolution fall-off is variance shared between them and lifts a false operator's correlation as much as a true one's; the screw-axis test scores a predicted-absent class against the rest of its own axial row rather than against a global mean or a fixed cut, and lets confidence fall away with the number of axial reflections instead of refusing below a count; the glide-plane test is that same test applied to a zone, scoring the extinguished class against the rest of its own plane, as POINTLESS scores zonal absences. P. Evans, "Scaling and assessment of data quality" (2006), Acta Cryst. D62, 72-82 doi:10.1107/S0907444905036693; P. R. Evans, "An introduction to data reduction: space-group determination, scaling and intensity statistics" (2011), Acta Cryst. D67, 282-292 doi:10.1107/S090744491003982X; P. R. Evans and G. N. Murshudov, "How good are my data and what is the resolution?" (2013), Acta Cryst. D69, 1204-1214 doi:10.1107/S0907444913000061; J. Agirre, M. Atanasova, H. Bagdonas et al., "The CCP4 suite: integrative software for macromolecular crystallography" (2023), Acta Cryst. D79, 449-461 doi:10.1107/S2059798323003595.

Baur and Kassner — the convention for which of two absence-equivalent glide groups the space-group search writes (P2/c over Pc, C2/c over Cc): the centrosymmetric one, because a missed inversion centre is the common error among published small-molecule space-group assignments. W. H. Baur and D. Kassner, "The perils of Cc: comparing the frequencies of falsely assigned space groups with their general population" (1992), Acta Cryst. B48, 356-369 doi:10.1107/S0108768191014726.

The centre-of-symmetry statistics are Wilson's and Howells, Phillips & Rogers's: the intensity distributions of acentric and centric structures and the cumulative N(z) test built on them, read here on the general reflections of the Laue class beside <|E^2-1|> and Padilla and Yeates's L test (taken at its centric value, 2/pi). A. J. C. Wilson, "The probability distribution of X-ray intensities" (1949), Acta Cryst. 2, 318-321 doi:10.1107/S0365110X49000813; E. R. Howells, D. C. Phillips and D. Rogers, "The probability distribution of X-ray intensities. II. Experimental investigation and the X-ray detection of centres of symmetry" (1950), Acta Cryst. 3, 210-214 doi:10.1107/S0365110X50000513.

The twinning L test is Padilla and Yeates's: pairing each acentric reflection with a symmetry-independent neighbour and reading the first and second moments of L = (I1−I2)/(I1+I2) against their untwinned and perfect-twin values. J. E. Padilla and T. O. Yeates, "A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning" (2003), Acta Cryst. D59, 1124-1130 doi:10.1107/S0907444903007947. Their title claims robustness to pseudo-centering, and this program's partner steps deliver it: a step of 2 along an axis preserves the class of a half-integer pseudo-translation, which is what a pseudo-centering is. That robustness does not extend to a pseudo-translation which is not half-integer, and the partner steps are restricted when one is detected - see the translational-pseudo-symmetry note below.

The twin fraction of the twin hypothesis, and the twinned model it is scored with, follow Yeates: the intensity a twinned crystal records is (1−α) I(h) + α I(Th), and the disagreement H = |I(h) − I(Th)|/(I(h) + I(Th)) of the pairs a law relates is uniform on [0, 1−2α], so the median gives the fraction. T. O. Yeates, "Detecting and overcoming crystal twinning" (1997), Methods Enzymol. 276, 344-358 doi:10.1016/S0076-6879(97)76068-3.

A first-pass cell that is the coincidence lattice of two twin domains (twinning by reticular merohedry of index 2 or 3, e.g. obverse/reverse rhombohedral domains or a cubic crystal twinned about [111]) is recognised by the nodes that belong to neither domain being empty. The twin index is Friedel's (G. Friedel, Leçons de cristallographie, 1926; no DOI); the split of the reflections into those of one domain, of the other, of both and of neither is the one Herbst-Irmer and Sheldrick use for obverse/reverse twins: R. Herbst-Irmer and G. M. Sheldrick, "Refinement of obverse/reverse twins" (2002), Acta Cryst. B58, 477-481 doi:10.1107/S0108768102001039.

Translational pseudo-symmetry is detected from the native Patterson computed from the merged intensities, and the interpretation of an off-origin peak as a pseudo-translation between copies of the contents of the asymmetric unit - together with the modulation it puts on the intensities, which is the second half of the test here - is Read, Adams and McCoy's. Their fitted peak-height table is not used: the peak is scored against a per-dataset within-shell permutation null instead, because the noise floor of the statistic depends strongly on how many reflections a dataset has. The same modulation is what the axial systematic-absence test scores against, so that a reflection class a pseudo-translation merely suppresses is not read as extinct and does not buy a screw axis; the estimate of its depth there is our own, measured per axial row from the merged intensities rather than from the Patterson vector. R. J. Read, P. D. Adams and A. J. McCoy, "Intensity statistics in the presence of translational noncrystallographic symmetry" (2013), Acta Cryst. D69, 176-183 doi:10.1107/S0907444912045374.

Scaling, merging and data quality

DIALS — the resolution cutoff from the CC1/2 fall-off, per-observation outlier rejection at merge, the scaling error model, and the treatment of a reflection whose background is contaminated. Its published behaviour, and in places its source, settled several choices here. G. Winter, D. G. Waterman, J. M. Parkhurst et al., "DIALS: implementation and evaluation of a new integration package" (2018), Acta Cryst. D74, 85-97 doi:10.1107/S2059798317017235; D. G. Waterman, G. Winter, R. J. Gildea et al., "Diffraction-geometry refinement in the DIALS framework" (2016), Acta Cryst. D72, 558-575 doi:10.1107/S2059798316002187; J. Beilsten-Edmands, G. Winter, R. Gildea et al., "Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling" (2020), Acta Cryst. D76, 385-399 doi:10.1107/S2059798320003198; J. M. Parkhurst, G. Winter, D. G. Waterman et al., "Robust background modelling in DIALS" (2016), J. Appl. Cryst. 49, 1912-1921 doi:10.1107/S1600576716013595.

Wilson outlier test — judging an observation that has no symmetry mates against the acentric and 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:10.1107/S0365110X49000813; P. Evans, "Scaling and assessment of data quality" (2006), Acta Cryst. D62, 72-82 doi:10.1107/S0907444905036693.

Amplitudes from intensities — the posterior-mean amplitude of each merged intensity under the acentric and centric Wilson priors is French and Wilson's; giving no amplitude to an intensity more than 3.7 sigma below zero, and leaving such intensities out of the prior, follows CCP4's ctruncate (C. Ballard and N. Stein). So does scaling each reflection's Wilson prior by the anisotropy tensor along its direction, which ctruncate has done by default since its version 1.7 ("use anisotropy in prior for truncate procedure"); rugnux uses its own tensor for it (see Diffraction anisotropy below). S. French and K. Wilson, "On the treatment of negative intensity observations" (1978), Acta Cryst. A34, 517-525 doi:10.1107/S0567739478001114; ctruncate is cited through the CCP4 suite: M. D. Winn, C. C. Ballard, K. D. Cowtan et al., "Overview of the CCP4 suite and current developments" (2011), Acta Cryst. D67, 235-242 doi:10.1107/S0907444910045749.

Absorption as spherical harmonics — describing an empirical absorption correction as a series of real spherical harmonics of the beam directions in the crystal frame is Blessing's; its use as a restrained scaling surface of the diffracted-beam direction follows SCALA and AIMLESS. R. H. Blessing, "An empirical correction for absorption anisotropy" (1995), Acta Cryst. A51, 33-38 doi:10.1107/S0108767394005726; P. Evans, "Scaling and assessment of data quality" (2006), Acta Cryst. D62, 72-82 doi:10.1107/S0907444905036693.

Diffraction anisotropy — the description of the overall fall-off by a single anisotropic displacement tensor, its symmetry constraints, and the fact that only its deviatoric part is determined (the isotropic part being degenerate with the overall scale) are Sheriff and Hendrickson's. The estimator fits that tensor to the observed intensity distribution, taking sigma(I) into account, in the sense of Popov and Bourenkov. The directional diffraction limits - <I/sigma(I)> in a cone about each principal direction, and the reporting of the anisotropic deltaB as the range of the principal components - follow AIMLESS. Rugnux reports these; it corrects no intensity and removes no reflection on a directional criterion. S. Sheriff and W. A. Hendrickson, "Description of overall anisotropy in diffraction from macromolecular crystals" (1987), Acta Cryst. A43, 118-121 doi:10.1107/S010876738709977X; A. N. Popov and G. P. Bourenkov, "Choice of data-collection parameters based on statistic modelling" (2003), Acta Cryst. D59, 1145-1153 doi:10.1107/S0907444903008163; P. R. Evans and G. N. Murshudov, "How good are my data and what is the resolution?" (2013), Acta Cryst. D69, 1204-1214 doi:10.1107/S0907444913000061.

Data-quality statistics follow the established conventions rather than any one program: R_meas and R_pim, CC1/2 and CC*, the per-shell CC(model, data) between F^2_calc and F^2_obs, and the reporting of I/sigma(I). K. Diederichs and P. A. Karplus, "Improved R-factors for diffraction data analysis in macromolecular crystallography" (1997), Nat. Struct. Biol. 4, 269-275 doi:10.1038/nsb0497-269; P. A. Karplus and K. Diederichs, "Linking crystallographic model and data quality" (2012), Science 336, 1030-1033 doi:10.1126/science.1218231; M. S. Weiss, "Global indicators of X-ray data quality" (2001), J. Appl. Cryst. 34, 130-135 doi:10.1107/S0021889800018227 (R_pim beside R_meas and R_merge); K. Diederichs and P. A. Karplus, "Better models by discarding data?" (2013), Acta Cryst. D69, 1215-1222 doi:10.1107/S0907444913001121.

The Whittaker smoother — the per-frame scale of the rotation fulls is a penalised least-squares 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; E. T. Whittaker, "On a new method of graduation" (1923), Proc. Edinburgh Math. Soc. 41, 63-75 doi: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 a multiplicative error shows, are not outweighed by the noise of the shells without signal. R. A. Fisher, "Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population" (1915), Biometrika 10, 507-521 doi:10.2307/2331838.

The frame disposition - which stretches of a rotation sweep are kept, carried at reduced weight or dropped from the merge - decides every exclusion on delta-CC1/2, the change in the overall CC1/2 when a group of images is left out, measured in the sigma-tau form so that no random half-dataset split is involved. The statistic, the Fisher transformation used to compare it across CC1/2 values, its standard error going as the inverse square root of the reflection count, and the rejection discipline (never remove a group whose delta-CC1/2 is positive or near zero; remove a little, re-form the reference and repeat) are all taken from its authors, whose XDSCC12 is the reference implementation. G. Assmann, W. Brehm and K. Diederichs, "Identification of rogue datasets in serial crystallography" (2016), J. Appl. Cryst. 49, 1021-1028 doi:10.1107/S1600576716005471; G. M. Assmann, M. Wang and K. Diederichs, "Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods" (2020), Acta Cryst. D76, 636-652 doi:10.1107/S2059798320006348. That the same statistic belongs at scaling, applied to groups of images rather than to whole datasets, follows DIALS (dials.scale, delta-CC1/2 image-group filtering): J. Beilsten-Edmands, G. Winter, R. Gildea et al., "Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling" (2020), Acta Cryst. D76, 385-399 doi:10.1107/S2059798320003198.

Uncertainty conventions follow the IUCr Commission on Crystallographic Nomenclature: D. Schwarzenbach, S. C. Abrahams, H. D. Flack et al., "Statistical descriptors in crystallography: Report of the IUCr Subcommittee on Statistical Descriptors" (1989), Acta Cryst. A45, 63-75 doi:10.1107/S0108767388009596; D. Schwarzenbach, S. C. Abrahams, H. D. Flack, E. Prince and A. J. C. Wilson, "Statistical descriptors in crystallography. II. Report of a Working Group on Expression of Uncertainty in Measurement" (1995), Acta Cryst. A51, 565-569 doi:10.1107/S0108767395002340.

Physical corrections and calibration

Sensor absorption at oblique incidence, and the flight path — the angle-dependent quantum efficiency of a flat sensor, the radial parallax variance that comes from the same integral, and the attenuation of a reflection in the air between the sample and its pixel are all the Beer-Lambert law taken along a ray that crosses t/cos(alpha) of sensor, or D/cos(alpha) of air, and converts at a random depth. The attenuation coefficients, for silicon, CdTe, dry air and helium alike, are the NIST tabulation: J. H. Hubbell and S. M. Seltzer, "Tables of X-Ray Mass Attenuation Coefficients and Mass Energy-Absorption Coefficients from 1 keV to 20 MeV for Elements Z = 1 to 92 and 48 Additional Substances of Dosimetric Interest" (1995, data updated 2004), NIST Standard Reference Database 126 doi:10.18434/T4D01F.

Polarization correction — the azimuthal polarization factor applied to the azimuthally integrated profile, to the integrated Bragg intensities and to the ring background the beam-stop shadow test compares a pixel against is the one derived for a partially polarized synchrotron source by R. Kahn, R. Fourme, A. Gadet, J. Janin, C. Dumas and D. Andre, "Macromolecular crystallography with synchrotron radiation: photographic data collection and polarization correction" (1982), J. Appl. Cryst. 15, 330-337 doi:10.1107/S0021889882012060.

Hexagonal-ice ring positions — the eleven ring d spacings from 3.895 to 1.522 Å that the ice-ring score, the ice-ring flagging and the ice calibrant are all built on are taken from the measurements of Moreau and co-workers, not enumerated from a cell. D. W. Moreau, H. Atakisi and R. E. Thorne, "Ice in biomolecular cryocrystallography" (2021), Acta Cryst. D77, 540-554 doi:10.1107/S2059798321001170.

That list ends at 1.522 Å by its own scope, so the eight bands below it are calculated here rather than taken from anyone: ice Ih structure factors on the oxygen sublattice, kept where they reach 3% of the strongest line, which reproduces the eleven measured positions exactly. The lattice constants are Röttger and co-workers'. K. Röttger, A. Endriss, J. Ihringer, S. Doyle and W. F. Kuhs, "Lattice constants and thermal expansion of H2O and D2O ice Ih between 10 and 265 K" (1994), Acta Cryst. B50, 644-648 doi:10.1107/S0108768194004933.

Model-based analysis and maps

Bulk-solvent correction and overall scaling — the model's structure factors are put on the observed scale with an overall factor, an anisotropic B and a flat bulk-solvent term, the flat-mask model of A. Fokine and A. Urzhumtsev, "Flat bulk-solvent model: obtaining optimal parameters" (2002), Acta Cryst. D58, 1387-1392 doi:10.1107/S0907444902010284, which is also the source of the starting values and of the range those two parameters are physically meaningful over. The procedure that fits them — a grid search over that range for the solvent pair, with the overall scale and the anisotropic B refitted at every grid point — follows P. V. Afonine, R. W. Grosse-Kunstleve and P. D. Adams, "A robust bulk-solvent correction and anisotropic scaling procedure" (2005), Acta Cryst. D61, 850-855 doi:10.1107/S0907444905007894. The fit is unweighted, as in both that procedure and REFMAC5: G. N. Murshudov, P. Skubak, A. A. Lebedev, N. S. Pannu, R. A. Steiner, R. A. Nicholls, M. D. Winn, F. Long and A. A. Vagin, "REFMAC5 for the refinement of macromolecular crystal structures" (2011), Acta Cryst. D67, 355-367 doi:10.1107/S0907444911001314.

sigma_A map coefficients — the maps written by --model are weighted by a maximum-likelihood sigma_A estimated per resolution shell, giving 2mFo-DFc and mFo-DFc rather than 2Fo-Fc and Fo-Fc. What is taken is the formalism itself: the Rice and Woolfson likelihoods of |Fo| given |Fc| and sigma_A, the figure of merit m and the scale D that follow from it, and the result that the bias-corrected coefficient is 2mFo-DFc for an acentric reflection and mFo for a centric one. R. J. Read, "Improved Fourier coefficients for maps using phases from partial structures with errors" (1986), Acta Cryst. A42, 140-149 doi:10.1107/S0108767386099622.

ANODE — reading the anomalous difference map at the atoms of a supplied model and reporting the strongest sites by name, instead of searching the map for blobs. The map itself is the textbook anomalous difference Fourier; what is taken from ANODE is that reading: A. Thorn and G. M. Sheldrick, "ANODE: anomalous and heavy-atom density calculation" (2011), J. Appl. Cryst. 44, 1285-1287 doi:10.1107/S0021889811041768.

Uniform random rotations — the null a supplied model is scored against re-orients that model at random about its own centroid, and the rotations are drawn uniformly from SO(3) through a uniform random unit quaternion. K. Shoemake, "Uniform Random Rotations", in Graphics Gems III, ed. D. Kirk, Academic Press (1992), 124-132 (no DOI).

Variable projection — the rigid-body placement of a supplied model re-fits the overall scale at every step, and its Jacobian folds that re-fit in by projecting the scale's own derivatives out of the placement's, in Kaufman's simplified form of Golub and Pereyra's derivative of the reduced problem. G. H. Golub and V. Pereyra, "The Differentiation of Pseudo-Inverses and Nonlinear Least Squares Problems Whose Variables Separate" (1973), SIAM J. Numer. Anal. 10, 413-432 doi:10.1137/0710036. L. Kaufman, "A variable projection method for solving separable nonlinear least squares problems" (1975), BIT 15, 49-57 doi:10.1007/BF01932995.

Software and computing methods

Decoding bitshuffle+LZ4 images on the GPU, rather than decompressing them on the host and uploading the result, follows Jon Wright (ESRF): "Experiences with GPU decompression for bitshuffle + LZ4 data", HDF5 User Group meeting (2021), and bslz4decoders. The CUDA kernels in Jungfraujoch are its own, but the approach is his.

Removing the small islands of solvent from the bulk-solvent mask on the GPU labels the connected components with a parallel union-find, following D. P. Playne and K. Hawick, "A New Algorithm for Parallel Connected-Component Labelling on GPUs" (2018), IEEE Trans. Parallel Distrib. Syst. 29, 1217-1230 doi:10.1109/TPDS.2018.2799216.

This software uses the Viridis, Magma and Inferno colormaps from Matplotlib under its BSD-compatible license. J. D. Hunter, "Matplotlib: A 2D graphics environment" (2007), Comput. Sci. Eng. 9, 90-95 doi:10.1109/MCSE.2007.55.

File formats read from a published specification

CBF / imgCIF - the native miniCBF reader implements the x-CBF_BYTE_OFFSET compression scheme and reads the imgCIF _axis table (the laboratory directions of the image's fast and slow pixel directions, of the goniometer axes and of a 2theta arm) from the specification alone; no CBFlib or other CBF code is used, so there is no licence obligation, only this credit. H. J. Bernstein and A. P. Hammersley, "Specification of the Crystallographic Binary File (CBF/imgCIF)" (2006), International Tables for Crystallography Vol. G, 37-43 doi:10.1107/97809553602060000729; A. P. Hammersley, H. J. Bernstein and J. D. Westbrook, "Image dictionary (imgCIF)" (2006), International Tables for Crystallography Vol. G, 444-458 doi:10.1107/97809553602060000746.

d*TREK SMV - the SMV reader reads the d*TREK header vocabulary written by Rigaku's CrystalClear (Saturn and R-AXIS detectors: detector and spatial-distortion vectors, detector circles, 2theta arm, encoded overflows) from the headers themselves, interpreting the detector vectors as dxtbx does for these detectors; no d*TREK or dxtbx code is used. J. W. Pflugrath, "The finer things in X-ray diffraction data collection" (1999), Acta Cryst. D55, 1718-1725 doi:10.1107/S090744499900935X; dxtbx: J. M. Parkhurst, A. S. Brewster, L. Fuentes-Montero, D. G. Waterman et al., "dxtbx: the diffraction experiment toolbox" (2014), J. Appl. Cryst. 47, 1459-1465 doi:10.1107/S1600576714011996.

Public diffraction data used for testing

In addition to in-house datasets collected at SLS 2.0, Jungfraujoch is tested against public diffraction data collected on other people's beamlines, on detectors and in file formats we do not produce ourselves - most of it at other facilities, a few sets at the Swiss Light Source but not by this system. That data was collected and published by other people. Every dataset used, the DOI to cite for it, and the deposition it belongs to are listed in EXTERNAL_TEST_DATA; we thank the depositors, and the repositories that make the data findable and citable.

IRRMC, the Integrated Resource for Reproducibility in Macromolecular Crystallography (Minor lab, University of Virginia), is the source of most of them. IRRMC releases its data under CC0 and asks that the DOI of the dataset be cited. M. Grabowski, K. M. Langner, M. Cymborowski, P. J. Porebski, P. Sroka, H. Zheng, D. R. Cooper, M. D. Zimmerman, M.-A. Elsliger, S. K. Burley and W. Minor, "A public database of macromolecular diffraction experiments" (2016), Acta Cryst. D72, 1181-1193 doi:10.1107/S2059798316014716; M. Grabowski, M. Cymborowski, P. J. Porebski, T. Osinski, I. G. Shabalin, D. R. Cooper and W. Minor, "The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years" (2019), Struct. Dyn. 6, 064301 doi:10.1063/1.5128672.

SBGrid Data Bank, the structural biology community's data publication service (SBGrid Consortium, Harvard Medical School). P. A. Meyer, S. Socias, J. Key, E. Ransey, E. C. Tjon, A. Buschiazzo et al., "Data publication with the structural biology data grid supports live analysis" (2016), Nat. Commun. 7, 10882 doi:10.1038/ncomms10882.

Zenodo, CERN's open repository, hosts datasets deposited there directly by the groups that collected them. European Organization for Nuclear Research and OpenAIRE, "Zenodo" (2013), CERN doi:10.25495/7GXK-RD71. Some of those deposits are described in IUCrData Raw Data Letters; the letters are cited on the EXTERNAL_TEST_DATA page, beside the datasets they describe.

MXRDR, the Macromolecular Xtallography Raw Data Repository (ICM, University of Warsaw), releases its data under CC0 and asks that the DOI of the dataset be cited.

XRDa, the Xtal Raw Data Archive (Protein Data Bank Japan), which publishes raw diffraction images - X-ray, electron and neutron - and mints a DOI for each; it asks that the DOI of the dataset be cited. It has no canonical citation paper.

The ESRF data portal, through which the European Synchrotron publishes raw data under its data policy (CC BY 4.0, with the dataset DOI to be cited). R. Dimper, A. Götz, A. De Maria, V. A. Solé, M. Chaillet and B. Lebayle, "ESRF Data Policy, Storage, and Services" (2019), Synchrotron Rad. News 32, 7-12 doi:10.1080/08940886.2019.1608119.

The Keele University research data repository and UQ eSpace (The University of Queensland), which host the raw images of datasets deposited there by the groups that collected them; the dataset DOIs are cited on the EXTERNAL_TEST_DATA page.

The beamline, resolution, space group and unit cell quoted for each dataset are the values deposited with the corresponding PDB entry, read from the RCSB PDB data API. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov and P. E. Bourne, "The Protein Data Bank" (2000), Nucleic Acids Res. 28, 235-242 doi:10.1093/nar/28.1.235.

Generative AI usage declaration

Large language models were used extensively in developing this code. Jungfraujoch development was supported with JetBrains AI (mostly GPT models) to refactor and verify particular code fragments. Rugnux was developed with the assistance of Claude Code (mostly the Opus model). This documentation was written with the assistance of Claude Opus and Fable models.