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leonarski_fandClaude Opus 5.5 fc6b91555f Merged mmCIF: deposition keys, R_merge/R_pim/CC*, experiment metadata, scaled unmerged block

The .cif now follows the PDBx/mmCIF dictionary's keys: _entry.id, the
entry_id of _cell/_symmetry/_reflns, pdbx_ordinal and pdbx_diffrn_id on
_reflns and _reflns_shell, diffrn_id on _diffrn_source/_diffrn_detector/
_diffrn_radiation, and _diffrn_radiation_wavelength.id. _software is a
loop naming Rugnux for 'data reduction' and for 'data scaling'.

The experiment as the input states it: _diffrn.ambient_temp from the
sample temperature, the source's general class (from NXmx
/entry/source/type, which the HDF5 reader now reads), facility and
beamline, the detector make/model in _diffrn_detector.type (where
.detector used to carry it) and its class in .detector where the name
settles it, and the collection date from /entry/start_time.

R_merge and R_pim are formed beside R_meas from the same per-reflection
sums (stills and rotation merges) and written with CC* overall and per
shell (_reflns.pdbx_Rmerge_I_obs/pdbx_Rpim_I_all/pdbx_CC_star and the
_reflns_shell counterparts), as report keys R_MERGE/R_PIM/CC_STAR and as
three new columns of the shell tables. R_pim following Weiss (2001),
CC* following Karplus & Diederichs (2012).

A second data block, data_sample_unmerged, carries the scaled unmerged
observations of a rotation merge as _diffrn_refln (measured index,
frame, scaled I and sigma, pdbx_scale_value) - the same records as the
.hkl, which the wwPDB accepts as scaled unmerged data. ScaledFull now
carries the scale and the frame. The unmerged MTZ stays unscaled.

Reflection data are unchanged: the merged _refln rows, the .mtz columns
and the .hkl are written as before.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi

2026-10-09 17:50:11 +02:00

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CPU-side crystallographic data analysis (Jungfraujoch)

This document describes the crystallographic algorithms implemented in Jungfraujoch for CPU- and GPU-side real‑time and near‑real‑time data analysis.

Scope. The pipeline covered here comprises:

geometry mapping and corrections,
azimuthal integration (powder/radial profiles),
Bragg spot finding (strong pixels → connected components → spot descriptors),
indexing (still and rotation modes),
Bravais lattice / centering inference,
geometry and lattice refinement,
reflection prediction (still and rotation),
Bragg integration by either 2D box summation or profile fitting (Kabsch, reference-free),
scaling and merging,
merge-level error modelling, outlier rejection and the resolution cutoff,
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,
auxiliary statistics (Wilson plot, ⟨I/σ(I)⟩, CC1/2, CCref),
amplitude estimation (French–Wilson) and R-free test-set flagging,
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.

The reference is split into four parts, in pipeline order; the section numbers run continuously across them and are the ones the rest of the documentation cites.

From images to spots (§0–§3) — device-side decoding, geometry and reciprocal-space mapping, azimuthal integration, spot finding.
Indexing and geometry refinement (§4–§7) — FFT and fast-feedback indexing, the lattice search, geometry refinement, post-refinement and powder calibration.
Prediction, integration, scaling and merging (§8–§12) — reflection prediction, profile-fitted integration, scaling, merging, mosaicity and the auxiliary statistics.
Space group and validation (§13–§14) — the space-group search, twinning and translational pseudo-symmetry, the resolution cutoff, diffraction anisotropy, and model-based validation.

References

The methods draw on, and in places reimplement, solutions from:

W. Kabsch, “XDS”, Acta Cryst. D66 (2010), 125–132 and related XDS papers (rotation geometry, partiality, scaling concepts).
W. Kabsch, “Integration, scaling, space-group assignment and post-refinement”, Acta Cryst. D66 (2010), 133–144 (mosaicity/partiality likelihood treatment; notation such as ζ and rotation factors).
T. A. White et al., CrystFEL method papers (spot finding, three‑ring integration, serial/still diffraction processing concepts).
J. Kieffer & J. P. Wright, "PyFAI: a Python library for high performance azimuthal integration on GPU", Powder Diffraction 28 (2013), S339-S350 (detector geometry definition, azimuthal integration)
I. Steller, R. Bolotovsky & M. G. Rossmann, "An algorithm for automatic indexing of oscillation images using Fourier analysis", J. Appl. Cryst. 30 (1997), 1036-1040 (the projection/1D-FFT autoindexing algorithm of §5).
H. Powell, "The Rossmann Fourier autoindexing algorithm in MOSFLM", Acta Cryst. D55 (1999), 1690-1695 (the MOSFLM implementation of it, whose practice is followed)
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).
S. French & K. Wilson, "On the treatment of negative intensity observations", Acta Cryst. A34 (1978), 517-525 (Bayesian amplitude estimation from intensities), and CCP4's ctruncate (C. Ballard & N. Stein), whose anisotropic Wilson prior §10.8 follows, cited through M. D. Winn et al., "Overview of the CCP4 suite and current developments", Acta Cryst. D67 (2011), 235-242.
A. T. Brünger, "Free R value: a novel statistical quantity for assessing the accuracy of crystal structures", Nature 355 (1992), 472-475 (R-free cross-validation).
P. H. C. Eilers, "A perfect smoother", Anal. Chem. 75 (2003), 3631-3636, after E. T. Whittaker, "On a new method of graduation", Proc. Edinburgh Math. Soc. 41 (1923), 63-75 (the penalised smoother of the fulls' per-frame scale, §10.6).
R. A. Fisher, "Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population", Biometrika 10 (1915), 507-521 (the z-transformation on which the correction surfaces' held-out half-set CC1/2 is compared).
M. Wojdyr, "GEMMI: A library for structural biology", J. Open Source Softw. 7 (2022), 4200 (model / structure-factor / map machinery used in §14).
J. P. Wright, "Experiences with GPU decompression for bitshuffle + LZ4 data", HDF5 User Group meeting (2021), and github.com/jonwright/bslz4decoders (device-side decoding of bitshuffle+LZ4 images, §0).
A. Thorn & G. M. Sheldrick, "ANODE: anomalous and heavy-atom density calculation", J. Appl. Cryst. 44 (2011), 1285-1287 (anomalous difference density read at the model's sites).
R. Kahn, R. Fourme, A. Gadet, J. Janin, C. Dumas & D. Andre, "Macromolecular crystallography with synchrotron radiation: photographic data collection and polarization correction", J. Appl. Cryst. 15 (1982), 330-337 (the azimuthal polarization factor of §2.2, applied to the azimuthal profile, the Bragg intensities and the ring background the beam-stop shadow test compares against).
R. J. Read, "Improved Fourier coefficients for maps using phases from partial structures with errors", Acta Cryst. A42 (1986), 140-149 (the sigma_A formalism and the m, D weighting of the map coefficients of §14.4).
A. Fokine & A. Urzhumtsev, "Flat bulk-solvent model: obtaining optimal parameters", Acta Cryst. D58 (2002), 1387-1392 (the flat bulk-solvent model, its optimal parameters and the range they are physically meaningful over, used when scaling a model to the data in §14).
P. V. Afonine, R. W. Grosse-Kunstleve & P. D. Adams, "A robust bulk-solvent correction and anisotropic scaling procedure", Acta Cryst. D61 (2005), 850-855 (the grid search over that range that fits k_sol and b_sol, with the overall scale and anisotropic B refitted at each grid point).
K. Shoemake, "Uniform Random Rotations", in Graphics Gems III, ed. D. Kirk, Academic Press (1992), 124-132 (the uniform random rotations the model-fit null of §14.5 is built from).
G. H. Golub & V. Pereyra, "The differentiation of pseudo-inverses and nonlinear least squares problems whose variables separate", SIAM J. Numer. Anal. 10 (1973), 413-432, and L. Kaufman, "A variable projection method for solving separable nonlinear least squares problems", BIT 15 (1975), 49-57 (the scale re-fit folded into the rigid-body Jacobian of §14.8).
Z. Otwinowski & W. Minor, "Processing of X-ray diffraction data collected in oscillation mode", Methods Enzymol. 276 (1997), 307-326 (reweighted, de-biased profile-fit variances).
G. Winter et al., "DIALS: implementation and evaluation of a new integration package", Acta Cryst. D74 (2018), 85-97, and J. Beilsten-Edmands et al., Acta Cryst. D76 (2020), 385-399 (CC1/2 resolution cutoff, merge outlier rejection, scaling error model).
R. H. Blessing, "An empirical correction for absorption anisotropy", Acta Cryst. A51 (1995), 33-38 (absorption as spherical harmonics of the beam directions).
P. Evans, "Scaling and assessment of data quality", Acta Cryst. D62 (2006), 72-82, and P. R. Evans, Acta Cryst. D67 (2011), 282-292 (POINTLESS: operator-by-operator point-group scoring, and the axial-zone screw-absence test).
A. G. W. Leslie & H. R. Powell, "Processing diffraction data with MOSFLM" (2007), NATO Science Series II 245, 41-51 (post-refinement practice: what is refined per image and what over a wedge).
D. W. Moreau, H. Atakisi & R. E. Thorne, "Ice in biomolecular cryocrystallography", Acta Cryst. D77 (2021), 540-554 (measured hexagonal-ice ring positions, used by the ice-ring score, the ice flagging and the ice calibrant).
K. Röttger, A. Endriss, J. Ihringer, S. Doyle & W. F. Kuhs, "Lattice constants and thermal expansion of H2O and D2O ice Ih between 10 and 265 K", Acta Cryst. B50 (1994), 644-648 (the ice Ih cell the ring positions below 1.522 Å are calculated from).
S. Sheriff & W. A. Hendrickson, "Description of overall anisotropy in diffraction from macromolecular crystals", Acta Cryst. A43 (1987), 118-121 (the overall anisotropic B tensor and its symmetry constraints), and A. N. Popov & G. P. Bourenkov, "Choice of data-collection parameters based on statistic modelling", Acta Cryst. D59 (2003), 1145-1153 (the sigma-aware estimation of the anisotropy of the observed intensity distribution, part of that paper's statistic modelling).
P. R. Evans & G. N. Murshudov, "How good are my data and what is the resolution?", Acta Cryst. D69 (2013), 1204-1214 (AIMLESS: the anisotropic deltaB as the range of the principal components, and diffraction limits from a cone about each principal direction).
G. Assmann, W. Brehm & K. Diederichs, "Identification of rogue datasets in serial crystallography", J. Appl. Cryst. 49 (2016), 1021-1028, and G. M. Assmann, M. Wang & K. Diederichs, Acta Cryst. D76 (2020), 636-652 (XDSCC12: sigma-tau CC1/2, delta-CC1/2, the Fisher transformation and the rejection discipline the frame disposition follows).
K. Diederichs & P. A. Karplus, Nat. Struct. Biol. 4 (1997), 269-275, and P. A. Karplus & K. Diederichs, Science 336 (2012), 1030-1033 (R_meas / R_pim, CC1/2 and CC*).
M. S. Weiss, "Global indicators of X-ray data quality", J. Appl. Cryst. 34 (2001), 130-135 (R_pim).
IUCr Commission on Crystallographic Nomenclature, "Statistical descriptors in crystallography", Acta Cryst. A45 (1989), 63-75, and Acta Cryst. A51 (1995), 565-569 (uncertainty conventions).

(list is not exhaustive; the full citations, with DOIs, are in ACKNOWLEDGEMENT.md)

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CPU-side crystallographic data analysis (Jungfraujoch)

References

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