diff --git a/ipsae.py b/ipsae.py
index 45f64de..2193b89 100644
--- a/ipsae.py
+++ b/ipsae.py
@@ -74,13 +74,17 @@
     af3 =    True
     boltz1 = False
     cif =    True
-elif ".cif" in pdb_path and pae_file_path.endswith(".npz"):
-    pdb_stem=pdb_path.replace(".cif","")
-    path_stem =     f'{pdb_path.replace(".cif","")}_{pae_string}_{dist_string}'
+elif (".cif" in pdb_path or ".pdb" in pdb_path) and pae_file_path.endswith(".npz"):
+    pdb_stem=pdb_path.replace(".cif","").replace(".pdb","")
+    # Determine extension for replacement
+    ext = ".cif" if ".cif" in pdb_path else ".pdb"
+    path_stem =     f'{pdb_path.replace(ext,"")}_{pae_string}_{dist_string}'
+    
     af2 =    False
     af3 =    False
     boltz1 = True
-    cif =    True
+    cif =    False # Set to False if using PDB so it uses the PDB parser
+    if ext == ".cif": cif = True
 else:
     print("Wrong PDB or PAE file type ", pdb_path)
     sys.exit()
@@ -216,7 +220,10 @@ def parse_cif_atom_line(line,fielddict):
     atom_num =        linelist[ fielddict['id'] ]
     atom_name =       linelist[ fielddict['label_atom_id'] ]
     residue_name =    linelist[ fielddict['label_comp_id'] ]
-    chain_id =        linelist[ fielddict['label_asym_id'] ]
+    if 'auth_asym_id' in fielddict:
+        chain_id = linelist[ fielddict['auth_asym_id'] ]
+    else:
+        chain_id = linelist[ fielddict['label_asym_id'] ]
     residue_seq_num = linelist[ fielddict['label_seq_id'] ]
     x =               linelist[ fielddict['Cartn_x'] ]
     y =               linelist[ fielddict['Cartn_y'] ]
@@ -441,7 +448,12 @@ def classify_chains(chains, residue_types):
     plddt_file_path=pae_file_path.replace("pae","plddt")
     if os.path.exists(plddt_file_path):
         data_plddt=np.load(plddt_file_path)
-        plddt_boltz1=np.array(100.0*data_plddt['plddt'])
+        raw_plddt = data_plddt['plddt']
+        # Only multiply by 100 if the max value is <= 1.0 (meaning it's normalized)
+        if np.max(raw_plddt) <= 1.0:
+            plddt_boltz1 = np.array(100.0 * raw_plddt)
+        else:
+            plddt_boltz1 = np.array(raw_plddt)
         plddt =    plddt_boltz1[np.ix_(token_array.astype(bool))]
         cb_plddt = plddt_boltz1[np.ix_(token_array.astype(bool))]
     else:
@@ -463,8 +475,12 @@ def classify_chains(chains, residue_types):
     if os.path.exists(summary_file_path):
         with open(summary_file_path, 'r') as file:
             data_summary = json.load(file)
-
-            boltz1_chain_pair_iptm_data=data_summary['pair_chains_iptm']
+            if 'pair_chains_iptm' in data_summary:
+                 boltz1_chain_pair_iptm_data=data_summary['pair_chains_iptm']
+            else:
+                 # Boltz2 specific or missing key fallback
+                 print(f"Warning: 'pair_chains_iptm' key not found in {summary_file_path}. ipTM scores will be 0.")
+                 boltz1_chain_pair_iptm_data = {}
             for chain1 in unique_chains:
                 nchain1=  ord(chain1) - ord('A')  # map A,B,C... to 0,1,2...
                 for chain2 in unique_chains:
@@ -967,4 +983,4 @@ def classify_chains(chains, residue_types):
         chain1_residues = f'chain  {chain1} and resi {contiguous_ranges(unique_residues_chain1[chain1][chain2])}'
         chain2_residues = f'chain  {chain2} and resi {contiguous_ranges(unique_residues_chain2[chain1][chain2])}'
         PML.write(f'alias {chain_pair}, color gray80, all; color {color1}, {chain1_residues}; color {color2}, {chain2_residues}\n\n')
-    OUT.write("\n")
+    OUT.write("\n")
\ No newline at end of file