Merge branch 'd-tncs-report' into rc172-2

image_analysis/scale_merge/TranslationalNCS.cpp

@@ -767,9 +767,12 @@ std::string TranslationalNCSToText(const TranslationalNCSResult &result) {
     os << "\n  [z = " << std::setprecision(1) << result.peak_z << " against a permutation null of "
        << result.null_mean << " +- " << std::setprecision(2) << result.null_sd << "%]\n";
     if (result.modulation_measured)
-        os << "  Intensity modulation along that vector: " << std::setprecision(1) << result.modulation
+        os << "  Intensity modulation: " << std::setprecision(1) << result.modulation
            << "x between the strongest and weakest phase class [random-vector control "
-           << result.modulation_null << "x]\n";
+           << result.modulation_null << "x]\n"
+           << "  [read on the search's own vector over d >= 4 A, which is what the control is drawn\n"
+           << "  against; the vector reported above is that one re-refined on the whole data, so it\n"
+           << "  points more accurately and this number is not re-read off it]\n";
     if (!result.modulation_measured) {
         os << "  The modulation test could not be run - too few acentric reflections beyond 4 A - so\n"
            << "  the peak above stands alone.\n"

rugnux/Rugnux.cpp

@@ -7502,9 +7502,21 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
                 // because it is folded under no symmetry, at full resolution and production-scaled.
                 // Report-only: nothing reads it back.
                 if (determined != nullptr && determined->number > 1) {
+                    // The pseudo-translation the zone is normalised by is measured on THIS merge, not
+                    // taken from `result.tncs`. That one is fitted on the adopted group's merge, and
+                    // where the pseudo-translation is not compatible with the adopted symmetry that
+                    // merge has already averaged across its own phase classes, so the vector fitted
+                    // there is poorly determined - measured on one crystal, the correlation between E^2
+                    // and cos(2 pi h.u) reads 0.04 on the group merge against 0.25 here, with the
+                    // optimum elsewhere entirely, and a vector that names the wrong classes normalises
+                    // the zone by noise. It is also the basis this merge is indexed on: a change of
+                    // basis committed by the search leaves a vector measured before it pointing
+                    // somewhere else.
+                    const auto p1_tncs = AnalyzeTranslationalNCS(
+                            p1.merged, gemmi::UnitCell(*result.consensus_cell));
                     result.twin_immune_zones = AnalyzeTwinImmuneZones(
                             p1.merged, gemmi::UnitCell(*result.consensus_cell), *determined,
-                            TranslationalNCSVectorForLTest(result.tncs));
+                            TranslationalNCSVectorForLTest(p1_tncs));
                     if (!result.twin_immune_zones->zones.empty())
                         logger.Info("{}", TwinImmuneZonesToText(*result.twin_immune_zones));
                 }