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>
85 lines
2.5 KiB
Python
85 lines
2.5 KiB
Python
# Configuration file for the Sphinx documentation builder.
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#
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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project = 'Jungfraujoch'
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copyright = '2024, Paul Scherrer Institute'
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author = 'Filip Leonarski'
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release = '1.0.0-rc.159'
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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'myst_parser',
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'sphinx.ext.mathjax',
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]
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templates_path = ['_templates']
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exclude_patterns = []
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myst_enable_extensions = [
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'linkify',
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'smartquotes',
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'dollarmath',
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'amsmath',
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]
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myst_heading_anchors = 3
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# The OpenAPI Python-client pages under docs/python_client/ are generated by the
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# openapi-generator and contain header-level jumps and intra-page anchors that MyST
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# cannot resolve. We do not hand-edit generated files, so silence that noise here;
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# the hand-written docs are anchor-clean once myst_heading_anchors is set above.
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# 'config.cache' fires only because the sphinx_material theme stores a function in
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# html_context, which is harmless for our single-shot builds.
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suppress_warnings = ['myst.header', 'myst.xref_missing', 'config.cache']
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# Render LaTeX-style math nicely in HTML and support AMS-style equation numbering.
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mathjax3_config = {
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"tex": {
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"tags": "ams",
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"inlineMath": [['\\(', '\\)'], ['$', '$']],
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"displayMath": [['\\[', '\\]'], ['$$', '$$']],
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"processEscapes": True,
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}
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}
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_theme = 'sphinx_material'
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html_static_path = ['../broker/redoc-static.html']
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#html_theme_options = {
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# 'sidebar_width': '300px',
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# 'page_width': 'auto'
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#}
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html_theme_options = {
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'repo_url': 'https://gitea.psi.ch/mx/jungfraujoch',
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'repo_name': 'Jungfraujoch',
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'nav_title': 'PSI Jungfraujoch',
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'html_minify': True,
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'css_minify': True,
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'globaltoc_depth': 2,
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'repo_type': 'gitlab',
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'color_primary': 'indigo',
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'color_accent': 'lime',
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'logo_icon': ''
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}
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html_logo = 'jfjoch.png'
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html_favicon = 'jfjoch.png'
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html_sidebars = {
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"**": ["logo-text.html", "globaltoc.html", "searchbox.html"]
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}
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html_show_sourcelink = False
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