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>

frontend/src/components/StatusBar.tsx

@@ -17,16 +17,15 @@ type MyProps = {
 }
 
 // A tight, strong palette: lime = good/running, coral = working/alarm (deeper = worse),
-// light-blue (sidebar) = neutral/idle-connection. Measuring is handled separately.
+// light-blue (sidebar) = neutral/idle-connection. Measuring and Pedestal are handled separately.
 const STATE_STYLE: Record<string, { fill: string; text: string }> = {
     Idle:      { fill: "secondary.main", text: "rgba(0,0,0,.87)" },   // lime + black text
     Busy:      { fill: deepOrange[300],  text: "rgba(0,0,0,.87)" },   // light coral
-    Pedestal:  { fill: deepOrange[300],  text: "rgba(0,0,0,.87)" },   // light coral
     Error:     { fill: deepOrange[700],  text: "#fff" },              // deep coral
     Inactive:  { fill: indigo[100],      text: "rgba(0,0,0,.87)" },   // sidebar light blue
 };
 
-// Fixed width so the pill fits the longest label ("Measuring · 100 %") and never
+// Fixed width so the pill fits the longest label ("Calibration · 100 %") and never
 // resizes as the state changes.
 const pillSx = {
     position: "relative", width: 200, height: 36, borderRadius: 999, overflow: "hidden",
@@ -57,16 +56,20 @@ function StatusChip({s}: {s?: broker_status}) {
             </Box>
         );
 
-    // Measuring: a light-blue (sidebar) track filled lime to the progress fraction,
-    // with black text that stays legible over both the track and the lime fill.
-    if (s.state === "Measuring") {
+    // Measuring and Pedestal both fill a light-blue (sidebar) track to the progress
+    // fraction, with black text legible over both track and fill. Measuring fills lime;
+    // Pedestal fills coral (matching its flat-pill colour elsewhere). The "Pedestal"
+    // state is shown as "Calibration" — the internal name is kept only for back-compat.
+    if (s.state === "Measuring" || s.state === "Pedestal") {
         const pct = Math.max(0, Math.min(100, (s.progress ?? 0) * 100.0));
+        const fill = s.state === "Measuring" ? "secondary.main" : deepOrange[300];
+        const label = s.state === "Measuring" ? "Measuring" : "Calibration";
         return (
             <Box sx={{...pillSx, bgcolor: indigo[100]}}>
                 <Box sx={{position: "absolute", left: 0, top: 0, bottom: 0, width: `${pct}%`,
-                          bgcolor: "secondary.main", transition: "width .4s ease"}}/>
+                          bgcolor: fill, transition: "width .4s ease"}}/>
                 <Typography component="span" sx={{...pillLabelSx, color: "rgba(0,0,0,.87)"}}>
-                    Measuring · {pct.toFixed(0)} %
+                    {label} · {pct.toFixed(0)} %
                 </Typography>
             </Box>
         );
@@ -114,7 +117,7 @@ function StatusBar({s, onMenuClick}: MyProps) {
                     {...TIER[cancelTier]}
                 />
                 <ButtonWithSnackbar
-                    text={"Pedestal"}
+                    text={"Calibrate"}
                     path={"/pedestal"}
                     disabled={!pedestalActive}
                     {...(pedestalActive ? TIER.active : TIER.off)}