leonarski_f
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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>
60 lines
1.8 KiB
C++
60 lines
1.8 KiB
C++
// Copyright 2020 Global Phasing Ltd.
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//
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// Interoperability between Model (MX) and SmallStructure (SX).
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#ifndef GEMMI_INTEROP_HPP_
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#define GEMMI_INTEROP_HPP_
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#include "model.hpp"
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#include "small.hpp"
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namespace gemmi {
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inline SmallStructure::Site atom_to_site(const Atom& atom, const UnitCell& cell) {
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SmallStructure::Site site;
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site.label = atom.name;
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site.type_symbol = atom.element.name();
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site.fract = cell.fractionalize(atom.pos);
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site.occ = atom.occ;
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// occupancy may need to be adjusted if the atom is on special position
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if (atom.occ <= 0.5) {
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int n_mates = cell.is_special_position(atom.pos);
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if (n_mates > 0 && atom.occ * (n_mates + 1) <= 1.0)
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site.occ = atom.occ * (n_mates + 1);
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}
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site.u_iso = atom.b_iso / u_to_b();
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if (atom.aniso.nonzero()) {
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if (cell.alpha == 90. || cell.beta == 90. || cell.gamma == 90.) {
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site.aniso = atom.aniso.scaled(1.0);
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} else {
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SMat33<double> t = atom.aniso.transformed_by<>(cell.frac.mat);
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Vec3 v = {1.0 / cell.ar, 1.0 / cell.br, 1.0 / cell.cr};
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site.aniso = {t.u11 * v.x * v.x,
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t.u22 * v.y * v.y,
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t.u33 * v.z * v.z,
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t.u12 * v.x * v.y,
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t.u13 * v.x * v.z,
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t.u23 * v.y * v.z};
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}
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}
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site.element = atom.element;
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site.charge = atom.charge;
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return site;
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}
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inline SmallStructure mx_to_sx_structure(const Structure& st, int n=0) {
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const Model& model = st.models.at(n);
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SmallStructure small_st;
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small_st.name = st.name;
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small_st.cell = st.cell;
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small_st.spacegroup_hm = st.spacegroup_hm;
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for (const Chain& chain : model.chains)
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for (const Residue& residue : chain.residues)
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for (const Atom& atom : residue.atoms)
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small_st.sites.push_back(atom_to_site(atom, st.cell));
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return small_st;
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}
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} // namespace gemmi
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#endif
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