diff --git a/main.py b/main.py
index 3fc5a7a..a6db2aa 100755
--- a/main.py
+++ b/main.py
@@ -17,6 +17,7 @@
 import os
 import sys
 import argparse
+import gemmi
 if __name__ == '__main__' and __package__ is None:
     sys.path.insert(1, os.path.dirname(os.path.dirname(os.path.abspath(__file__
                                                                        ))))
@@ -47,6 +48,36 @@
 GOOD_FINAL_RFREE = 0.4
 
 def dimple(wf, opt):
+
+    # --- START ALPHAFOLD PRE-PROCESSOR FIX ---
+    for i, pdb_path in enumerate(opt.pdbs):
+        if os.path.isfile(pdb_path):
+            try:
+                pdb_st = gemmi.read_structure(pdb_path)
+
+                # Check for the AlphaFold dummy cell (a-axis <2)
+                if pdb_st.cell.a < 2.0:
+                    # Assign a safe, massive dummy cell
+                    # Volume = 1,000,000 A^3. rwcontents won't crash
+                    # It will NOT match the MTZ, forcing dimple to use the phaser-mr path
+                    pdb_st.cell = gemmi.UnitCell(100.0, 100.0, 100.0, 90.0, 90.0, 90.0)
+                    pdb_st.spacegroup_hm = 'P 1'
+
+                    # Write to the absolute path of the output directory
+                    new_filename = "fixed_AF_" + os.path.basename(pdb_path)
+                    absolute_out_dir = os.path.abspath(opt.output_dir)
+                    fixed_path = os.path.join(absolute_out_dir, new_filename)
+                    pdb_st.write_pdb(fixed_path)
+                    
+                    # Update Dimple's internal list to use the new patched file
+                    opt.pdbs[i] = fixed_path
+
+            except Exception as e:
+                # If gemmi fails for any reason, print a warning but don't crash
+                print(f"[*] Pre-processor warning: Could not read PDB with Gemmi ({e}). Proceeding...")
+    # --- END ALPHAFOLD PRE-PROCESSOR FIX ---            
+
+    
     comment('     ### Dimple v%s. Problems and suggestions:'
             ' ccp4.github.io/dimple ###' % __version__)
     mtz_meta = wf.read_mtz_metadata(opt.mtz)