11 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	f077320efa	Refinement restraints: n_slots, not slots - Qt defines slots as a macro, which broke the viewer's build through Rugnux.h ... Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu	2026-10-25 10:22:02 +01:00
leonarski_f	789bd37606	Refinement: ten short macro-cycles instead of five long ones ... The scale, the bulk solvent and the likelihood's parameters are held within a macro-cycle; refitting them twice as often, with 10 L-BFGS iterations on the positions and 5 on B per cycle (was 25 and 15), lowered R-free on a 1.65 A deposited model from 0.2218 to 0.2189 with B held, and halved what B refinement cost there, at the same number of evaluations. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 8021d0cfc0bd56b1cc149a40df72ed78f35367c8)	2026-10-25 07:20:32 +01:00
leonarski_f	9cb5cc6237	Refinement: placement steps kept only where R-free drops; a wider weight ladder ... On deposited models the per-residue B shift raised R-free at every resolution tried (2.56 A: 0.320 -> 0.327) and the rigid bodies rarely helped; each is now kept only where it lowers R-free by more than the 0.001 tie, otherwise the model goes on as it was. The positions' weight ladder runs from 1/1024 to 1/32 of the gradient-balanced weight: the R-free optimum sat near 1/500 at 2.6 A and near 1/50 at 1.1-1.7 A. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit d444fb03f610db70903de04f53f0489a71540b37)	2026-10-25 07:20:32 +01:00
leonarski_f	a3082c1500	DensityBlobs: an ion is called by its anomalous peak alone; ligand size scales gentler with resolution ... Measured by stripping the deposited ligands and ions of 12 open-arm models (placement-refined, then the blobs of mFo-DFc): ligands with a blob 34/39, called LIGAND 26/39, LIGAND blobs on a removed ligand or ion 24/33; ions with a blob 23/40. The ligand-size threshold was four resolution spheres, which called no glycan at 3.3 A and every ion at 1.1 A; it is now one and a half, and never under 8 A^3. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 8e66d58ba87c35119df3ba8779ca193053f5cf00)	2026-10-25 07:20:32 +01:00
leonarski_f	b4b68d368f	Restrained refinement on the GPU: ML amplitude target, FFT gradient, dictionary restraints, R1 + R2 driver, blobs ... RefineModel (Refinement.h) refines a placed model against the merge, reading and writing nothing: - placement stage (R1): every chain of 50+ atoms as a rigid body at once (L-BFGS on six parameters per chain, their gradient from the per-atom one through Ceres jets), then one B shift per residue; - restrained stage (R2): positions and isotropic B of every atom of a residue the embedded dictionary describes, the rest held fixed but kept in Fcalc and the mask; riding hydrogens added by gemmi's topology, moved with their parents, re-placed every macro-cycle. Macro-cycles refit the mask, the scale and bulk solvent (FitModelScale / ModelScaleGPUPool) and the likelihood's D and beta (ML on the free set in resolution bins), rebuild the repulsion pairs (symmetry mates included), then L-BFGS on positions and, where chosen, on B. - weights: a ladder of full refinements at multiples of the gradient-balanced X-ray weight, chosen by R-free within bond/angle bounds (ties to the tighter geometry), then the B refinement tried at its own weights and kept only where it beats B held by more than the tie. The target and its gradient (RefinementXray, RefinementGPU): the Rice/centric amplitude likelihood (RefinementMath.h, shared host/device code), the gradient by Agarwal's FFT method - the adjoint of the reciprocal-space symmetry composition into a half-l (CPU) or half-u (cuFFT) spectrum, one inverse real transform, then each atom's density derivatives (xyz and B) summed over its box. On the GPU everything per evaluation stays on the device: ModelDensityGPU's gather, r2c, a fused compose + likelihood kernel, a CSR gather for the adjoint (no atomics), c2r, one warp per atom for the gradient; the restraints are one kernel per restraint plus a per-atom gather of gradient slots; cub reductions. Deterministic. Restraints (RefinementRestraints): bonds, angles, torsions (with esd, no phi/psi, no alternative sugar puckers), chiral volumes, least-squares planes from gemmi's Topo; repulsions beyond 1-4 (vdW radii from the dictionary's energy library, 2.6 A for H-bond pairs, 1.9 A metal-N/O/S); B similarity of bonded and angle-related atoms. DensityBlobs (D1): gemmi's flood-fill blobs of mFo-DFc above 3 sigma peaking above 4 sigma, placed beside the model and labelled WATER / ION / LIGAND / MODEL_ERROR by distance, contacts, volume and the anomalous map. tools/rugnux_refine_test refines a model against a finished run's p.mtz (developer utility, not installed). Tests: likelihood derivative, the embedded library, restraint values on ideal residues and every restraint kind's gradient against finite differences (CPU, and the GPU against the CPU), the X-ray gradient against finite differences in P1, P212121, C2 and P6122 (CPU and GPU), and a synthetic refinement that recovers a shaken model. Credits in docs/ACKNOWLEDGEMENT.md and at the algorithms. Measured on the open arm's battery outputs against REFMAC 5.8, 10 cycles, same p.mtz, free set and start model (R-free): 5reo 0.2228 vs 0.2236, 8dyz 0.1733 vs 0.1651, 9chw 0.1995 vs 0.1969 (CPU engine). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 8efe6f2322b3bfdae580bb34f256e67730dfc3c2)	2026-10-25 07:20:32 +01:00
leonarski_f	e58453a693	Refinement restraints: the CCP4 Monomer Library subset embedded in rugnux, read through gemmi's MonLib ... A restraint dictionary carried in the binary, so refinement reads nothing from disk and needs no CLIBD_MON: the 20 amino acids and MSE, the DNA/RNA nucleotides, ATP/ADP/AMP/GTP/GDP/GMP, DMSO, PEG fragments (PEG, PGE, PG4, 1PE), GOL, EDO, SO4, PO4, ACT, MPD, water and common ions - copied verbatim from the CCP4 Monomer Library (LGPL-3.0) - plus links_and_mods.cif cut down to the links and modifications those compounds can take (peptide, cis-peptide, proline, N-methyl, disulfide, nucleic-acid backbone, termini, metal-Cys/His) and ener_lib.cif cut to its atom-type table. monomers/update_monomers.py holds the compound list and regenerates the subset; CMake embeds every .cif of the directory as string pieces under MSVC's literal limit; EmbeddedMonomerLibrary() parses them from memory into a gemmi::MonLib once per process. About 0.7 MB of text in the binary. gemmi v0.7.5's monlib.cpp, topo.cpp and riding_h.cpp vendored verbatim (prepare_topology). Licence text in licenses/, rows and a note in THIRD_PARTY_NOTICES.md. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 38034718052c4a300691393b5b817f476c83dfc2)	2026-10-25 07:20:32 +01:00
leonarski_f	b00c668e3a	v1.0.0-rc.179 (#90) ... * Rugnux: Stills processing needs only the unit cell and space group beyond what the file records - detector distance, beam centre, tilt, panel placement, saturation level, gain and polarisation plane are found from the images - and is up to twice as fast. * Rugnux: Stills can be indexed without a GPU, with a CPU implementation of the fast-feedback indexer (macOS, computers without a GPU). * Rugnux: Rotation and stills data are integrated in the detector's own units with one gain model, improving data from CCD detectors. * Web frontend: The Rugnux live page shows the placed model with its electron density and anomalous difference map in a Mol* viewer. Reviewed-on: #90 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-24 14:52:29 +02:00
leonarski_f	afbe844b20	v1.0.0-rc.178 (#88) ... * Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`). * Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels. * Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL. * jfjoch_viewer: Opens the same XFEL file formats. * Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL. * Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded. * jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start. Reviewed-on: #88 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-21 11:20:01 +02:00
leonarski_f	7ed32b899f	v1.0.0-rc.177 (#87) ... * jfjoch_broker: Faster live Rugnux analysis, with the GPU indexers prepared at the start of a collection and kept between collections; Rugnux no longer writes `.ccp4` maps (the map coefficients are in `<prefix>_maps.mtz`). Reviewed-on: #87 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-19 16:07:31 +02:00
leonarski_f	8261b7354e	v1.0.0-rc.176 (#86) ... * jfjoch_broker: Optional live Rugnux analysis of DECTRIS rotation collections inside the broker, with merged data, maps and the placed model written beside the master file, the rotation lattice in the scan result, and a "Rugnux live" tab and dashboard row in the web frontend. * Rugnux: Faster processing, with molecular replacement and model validation spread over several GPUs and run on the Apple GPU on macOS. * Rugnux: The polarization stated in miniCBF and d*TREK headers is used, twinned crystals' space groups are decided more reliably, and a run that finds no lattice still reports every image. Reviewed-on: #86 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-19 07:03:28 +02:00
leonarski_fandFilip Leonarski	19b135186d	v1.0.0-rc.175 (#85) ... * Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-10-16 15:34:43 +02:00