script dump

model_vectors.py

@@ -0,0 +1,104 @@
+import gemmi
+import numpy as np
+import matplotlib.pyplot as plt
+# -----------------------------
+# User inputs
+# -----------------------------
+apo_pdb   = "../data/hewl_apo.pdb"
+occ100_pdb = "../data/hewl_1.0-I.pdb"
+occb_pdb  = "../data/hewl_0.5-I.pdb"
+
+b = 0.5
+a = 1.0 - b
+dmin = 2.0   # resolution cutoff (Å)
+
+# -----------------------------
+# Compute structure factors
+# -----------------------------
+def compute_sf(pdb_file, dmin):
+    # Read structure
+    st = gemmi.read_structure(pdb_file)
+    st.setup_entities()
+    st.assign_label_seq_id()
+    st.remove_alternative_conformations()
+
+    model = st[0]
+    cell = st.cell
+
+    # Space group
+    sg = st.find_spacegroup()
+    if sg is None:
+        if st.spacegroup_hm:
+            sg = gemmi.SpaceGroup(st.spacegroup_hm)
+        else:
+            raise RuntimeError("No space group found")
+
+    # Generate HKLs
+    hkl = gemmi.make_miller_array(
+        cell=cell,
+        spacegroup=sg,
+        dmin=dmin,
+        unique=True
+    )
+
+    # Structure factor calculator
+    calc = gemmi.StructureFactorCalculatorX(cell)
+
+    # Compute SFs ONE reflection at a time (this is required)
+    F = np.array([
+        calc.calculate_sf_from_model(model, [int(h), int(k), int(l)])
+        for h, k, l in hkl
+    ], dtype=np.complex128)
+
+    return hkl, F
+
+
+hkl, Fa = compute_sf(apo_pdb, dmin)
+_,   F100 = compute_sf(occ100_pdb, dmin)
+_,   Fb_model = compute_sf(occb_pdb, dmin)
+
+# -----------------------------
+# Sanity: same HKLs?
+# -----------------------------
+assert len(Fa) == len(F100) == len(Fb_model)
+
+# -----------------------------
+# Test forward relation:
+# Fab = a Fa + b F100
+# -----------------------------
+Fab = a * Fa + b * F100
+print(Fab)
+
+# Compare to model b-occupancy SFs
+delta_forward = Fab - Fb_model
+
+print("FORWARD TEST: Fab = aFa + bF100")
+print("Mean |ΔF|:", np.mean(np.abs(delta_forward)))
+print("Mean phase Δ (deg):",
+      np.mean(np.abs(np.angle(Fab / Fb_model, deg=True))))
+
+# -----------------------------
+# Test inverse relation:
+# F100 = (Fab − Fa) / b
+# -----------------------------
+F100_recon = (Fb_model - Fa) / b + Fa
+
+delta_inverse = F100_recon - F100
+
+print("\nINVERSE TEST: F100 = (Fab − Fa)/b + Fa")
+print("Mean |ΔF|:", np.mean(np.abs(delta_inverse)))
+print("Mean phase Δ (deg):",
+      np.mean(np.abs(np.angle(F100_recon / F100, deg=True))))
+
+# -----------------------------
+# Optional: inspect worst reflections
+# -----------------------------
+idx = np.argsort(np.abs(delta_inverse))[-5:]
+
+print("\nWorst reflections (inverse):")
+for i in idx:
+    print(
+        f"|F100|={abs(F100[i]):.2f}  "
+        f"|ΔF|={abs(delta_inverse[i]):.2f}  "
+        f"Δφ={np.angle(F100_recon[i]/F100[i],deg=True):.1f}°"
+    )