leonarski_f
dd0bffb283
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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
66 lines
1.8 KiB
JSON
66 lines
1.8 KiB
JSON
{
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"name": "jungfraujoch-frontend",
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"version": "1.0.0-rc.159",
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"license": "GPL-3.0",
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"private": true,
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"homepage": "/frontend",
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"type": "module",
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"dependencies": {
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"@emotion/react": "^11.10.4",
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"@emotion/styled": "^11.10.4",
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"@mui/icons-material": "^6.1.2",
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"@mui/material": "^6.1.2",
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"@mui/x-data-grid": "^7.19.0",
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"@tanstack/react-query": "^5.101.0",
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"@types/node": "^25.2.3",
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"@types/react": "^19.2.14",
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"@types/react-dom": "^19.2.3",
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"@vitejs/plugin-react-swc": "^4.2.3",
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"lodash": "^4.17.23",
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"plotly.js-cartesian-dist-min": "^3.3.1",
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"react": "^19.2.4",
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"react-dom": "^19.2.4",
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"react-markdown": "^10.1.0",
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"react-plotly.js": "^2.6.0",
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"react-zoom-pan-pinch": "^3.4.3",
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"remark-gfm": "^4.0.1",
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"typescript": "^5.9.3",
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"vite": "^7.3.1",
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"vite-plugin-svgr": "^4.5.0",
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"vite-tsconfig-paths": "^6.1.1",
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"zod": "^4.4.3"
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},
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"scripts": {
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"start": "vite",
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"build": "tsc && vite build",
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"serve": "vite preview",
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"redocly": "redocly build-docs ../broker/jfjoch_api.yaml --output=dist/openapi.html",
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"docs": "bash ../make_doc.sh dist/docs",
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"redocly4broker": "redocly build-docs ../broker/jfjoch_api.yaml --output=../broker/redoc-static.html",
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"licenses": "node scripts/generate-third-party-licenses.mjs",
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"openapi": "openapi-ts"
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},
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"overrides": {
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"styled-components": "5.3.11"
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},
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"browserslist": {
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"production": [
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">0.2%",
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"not dead",
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"not op_mini all"
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],
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"development": [
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"last 1 chrome version",
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"last 1 firefox version",
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"last 1 safari version"
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]
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},
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"devDependencies": {
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"@hey-api/openapi-ts": "^0.98.2",
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"@redocly/cli": "^2.28.1",
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"@types/lodash": "^4.17.10",
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"@types/react-plotly.js": "^2.6.3",
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"esbuild-style-plugin": "^1.6.3"
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}
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}
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