Fixes from Claude Code (to be tested)

image_analysis/IndexAndRefine.cpp

@@ -120,14 +120,16 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
                 outcome.lattice_candidate = sym_result.conventional;
             }
 
-            // Multi-lattice search for stills: keep extra lattices that share the
-            // reference unit cell but differ only in orientation. Quick refinement
-            // (orientation only) is done later in RefineGeometryIfNeeded.
+            // Multi-lattice search for stills: store rotations that map the reference
+            // lattice to each accepted extra lattice. Candidates are materialized later
+            // in RefineGeometryIfNeeded so they're rooted in the refined (and, for
+            // monoclinic, reordered) main lattice.
             if (indexer_result.lattice.size() > 1) {
                 auto ml_latt = MultiLatticeSearch(indexer_result.lattice);
                 for (auto &ml : ml_latt) {
-                    if (outcome.extra_lattice_candidates.size() >= experiment.GetIndexingSettings().GetMaxExtraLattices())
+                    if (outcome.extra_lattice_rotations.size() >= experiment.GetIndexingSettings().GetMaxExtraLattices())
                         break;
+                    outcome.extra_lattice_rotations.push_back(ml.rotation_vector);
                     RotMatrix rot(ml.rotation_vector.Length(), ml.rotation_vector.Normalize());
                     outcome.extra_lattice_candidates.push_back(outcome.lattice_candidate->Multiply(rot));
                 }
@@ -186,6 +188,17 @@ void IndexAndRefine::RefineGeometryIfNeeded(DataMessage &msg, IndexAndRefine::In
     if (outcome.symmetry.crystal_system == gemmi::CrystalSystem::Monoclinic)
         outcome.lattice_candidate->ReorderMonoclinic();
 
+    // Rebuild extra-lattice candidates from the refined (and possibly reordered) main
+    // lattice so they share its cell and obtuse-beta convention.
+    if (!outcome.extra_lattice_rotations.empty()) {
+        outcome.extra_lattice_candidates.clear();
+        outcome.extra_lattice_candidates.reserve(outcome.extra_lattice_rotations.size());
+        for (const auto &rv : outcome.extra_lattice_rotations) {
+            RotMatrix rot(rv.Length(), rv.Normalize());
+            outcome.extra_lattice_candidates.push_back(outcome.lattice_candidate->Multiply(rot));
+        }
+    }
+
     // Quick orientation-only refinement of extra lattices (stills path).
     // Cell, beam center, detector geometry are taken from the first lattice.
     if (!experiment.IsRotationIndexing() && !outcome.extra_lattice_candidates.empty()) {