visualize.py: opaque mesh (0.55) + opaque beads + white wireframe + xyz axis labels

visualize.py

@@ -532,7 +532,7 @@ def create_3d_visualization(
                 'vertexArr': vertex_arr,
                 'faceArr': face_arr,
                 'color': '#fbbf24',  # warm Mercury-style yellow
-                'opacity': 0.25,
+                'opacity': 0.55,
             })
         except Exception:
             # Mesh shape construction failed (e.g. py3Dmol API mismatch on
@@ -568,12 +568,27 @@ def create_3d_visualization(
                                'z': float(centre[2])},
                     'radius': float(bead_radius),
                     'color': color,
-                    'opacity': 0.95,
+                    'opacity': 1.0,
                 })
                 shown += 1
 
-    # Unit cell wireframe (light grey so it stays visible on black bg)
-    view.addUnitCell({'box': {'color': 'rgba(255,255,255,0.45)'}})
+    # Unit cell: white wireframe so the crystal lattice boundary is visible
+    # on the black background. The default red/green/blue axis arrows are
+    # hidden and replaced with simple x/y/z labels at the axis tips.
+    label_style = {'fontColor': 'white', 'fontSize': 14,
+                   'showBackground': False}
+    view.addUnitCell({
+        'box': {'color': 'rgba(255,255,255,0.7)'},
+        'astyle': {'hidden': True},
+        'bstyle': {'hidden': True},
+        'cstyle': {'hidden': True},
+        'alabel': 'x',
+        'blabel': 'y',
+        'clabel': 'z',
+        'alabelstyle': label_style,
+        'blabelstyle': label_style,
+        'clabelstyle': label_style,
+    })
 
     # Compute attribution scale so the hover label can de-scale B-factor back to
     # the original signed attribution value the user understands.