2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	f7cb701f43	rugnux: let --model settle the indexing of the reflections it writes ... ValidateAgainstModel was called after WriteReflections, so the two relabelings it makes - the change of hand where the data were merged in the model's enantiomorph, and the alternative indexing it picks by R-free where no reference MTZ had already fixed it - reached the R-factors, the maps and _maps.mtz and nothing else. The .mtz/.cif/.hkl beside them kept whichever indexing the merge happened to land in, so a file whose maps came from a model could not be refined against that model without being reindexed first. Validation now runs before the reflection files are written and returns the operators it applied. AdoptModelFrame puts the merged reflections through them with a proper ASU reduction - ReindexReflections only relabels, which is all its scoring callers need - and the Bijvoet halves follow the Friedel sign of that reduction. The integrated observations are relabelled too, so --export-unmerged describes the same indexing as the merged files rather than a second one. change_of_hand_op is the inversion, so adopting a model's hand exchanges I(+) and I(-). On a tetragonal crystal whose enantiomorphic pair share their whole absence pattern, the search picks one of the two arbitrarily, and the exported anomalous differences were the wrong way round whenever it picked the other member from the model's. The written space group follows the hand, and so does the report that describes those files. The _process.h5 is deliberately left alone: its per-image reflections went to disk as they were integrated, and recording a group that did not match them would mis-merge on a later --mode scale. Nothing is lost - an enantiomorphic pair has the same Laue class and the same absences, so it merges identically either way. Serial stills could not use a model for this at all: each crystal is indexed in its own hand, so by the time there is a merge to fit a model to, the hands have already been averaged together, and reindexing the merged result as a whole cannot separate them again. ModelReferenceIntensities computes |F_model|^2 from the structure - Fcalc plus a flat solvent term at the standard constants, which are not fitted because there are no observations yet - and hands it to the per-image resolver that a reference MTZ already drove. It needs the cell and the group up front, which serial indexing wants anyway. Measured on a serial dataset in a merohedral trigonal group, at a fixed resolution limit so the shells match: CC1/2 better in 8 of 10 shells (79.7 to 82.5 overall), R_meas better in 9 of 10 (111.1 to 104.7), ISa 1.11 to 1.20, and R-free against a structure the merge never saw 0.393 to 0.375. The ambiguity probe now logs the runner-up R-free as well as the winner. On the same data the margin is 0.016 when the hands are mixed, where the two global indexings are tied because both are already inside every reflection, and 0.193 once they are not - the difference between a decision and a coin toss, which the old single number hid. The warning about an unresolved ambiguity no longer fires when a model will resolve it, and names the flags that would; and the summary line no longer offers the adopted group as its own alternative, which it did once --model had moved the run onto the member the search had listed as the alternative. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Vi1gV6Z45aZL5wLwe85Ksn	2026-08-26 20:04:02 +02:00
leonarski_f	dd0bffb283	v1.0.0-rc.159 (#69) ... 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>	2026-07-13 13:54:03 +02:00