Polyhedra-style aesthetic: indigo metal SBUs

visualize.py

@@ -251,44 +251,45 @@ def create_3d_visualization(
     view = py3Dmol.view(width=width, height=height)
     view.addModel(cif_str, 'cif')
 
-    # Element coloring: standard Jmol chemistry palette (Cu=copper, O=red, N=blue, C=gray, H=white).
-    # The bfactor encodes attribution magnitude in the downloadable iRASPA CIF; the live 3D viewer
-    # uses element colors for clarity (the per-atom attribution magnitudes are reported in the
-    # "Top contributing atoms" strip below the viewer and in the Trustworthiness tab).
-    bfactor_style = {'colorscheme': 'Jmol'}
+    # Polyhedra-style aesthetic: metals as bold blue spheres (the SBU centers),
+    # other atoms as smaller spheres in soft gray shades. Inspired by iRASPA /
+    # crystal-toolkit visualisation conventions where metal SBUs are blue
+    # polyhedra and the linker network sits behind in muted tones.
+    metal_style = {'color': '#1e3a8a'}        # deep indigo for metal SBUs
+    nonmetal_style = {'colorscheme': 'Jmol'}  # standard chemistry colors
+    bfactor_style = nonmetal_style             # name retained for downstream code paths
 
     # Determine which elements are present in the structure
     elements_present = set(str(site.specie) for site in structure)
     metals_present = sorted(elements_present & _METAL_ELEMENTS)
     nonmetals_present = sorted(elements_present - _METAL_ELEMENTS)
 
-    # Combined ball-and-stick representation. 3Dmol auto-computes bonds for
-    # CIF models from interatomic distances; the stick style draws those bonds.
+    # Default: ball-and-stick with Jmol coloring for non-metal framework atoms
     view.setStyle(
         {},
         {
-            'sphere': {'radius': 0.28, **bfactor_style},
-            'stick':  {'radius': 0.12, **bfactor_style},
+            'sphere': {'radius': 0.28, **nonmetal_style},
+            'stick':  {'radius': 0.12, **nonmetal_style},
         },
     )
 
-    # Metal atoms: larger spheres to visually mark SBU centers
+    # Metal SBU centers: large indigo spheres to visually mark the polyhedra
     if metals_present:
         view.setStyle(
             {'elem': metals_present},
             {
-                'sphere': {'radius': 0.55, **bfactor_style},
-                'stick':  {'radius': 0.12, **bfactor_style},
+                'sphere': {'radius': 0.85, **metal_style},
+                'stick':  {'radius': 0.16, **metal_style},
             },
         )
 
-    # Hydrogens: smaller spheres so they do not dominate the view
+    # Hydrogens: tiny spheres so they do not dominate the view
     if 'H' in nonmetals_present:
         view.setStyle(
             {'elem': 'H'},
             {
-                'sphere': {'radius': 0.16, **bfactor_style},
-                'stick':  {'radius': 0.08, **bfactor_style},
+                'sphere': {'radius': 0.14, **nonmetal_style},
+                'stick':  {'radius': 0.06, **nonmetal_style},
             },
         )