diff --git a/barrOs_library.py b/barrOs_library.py
index 830402bf1219a13102338379edb57074b19c3239..f666a0ae3eef4a80b4f0303b344363d2eba5fffa 100644
--- a/barrOs_library.py
+++ b/barrOs_library.py
@@ -2302,7 +2302,10 @@ def run_barros(arguments, offset = 1, step = 2, local_angle_threshold = 25, dist
             target_chains = []
             if len(chains_inpdb) > 1:
                 for chainID in chains_inpdb:
-                    chain_pdb, protein_type, membrane_thickness = download_pdb('{}_{}'.format(pdbID.split('_')[0], chainID))
+                    if input_mode == 'pdb_file':
+                        chain_pdb, _ = extract_chain(pdb_file, chain, outpdb = 'downloaded_pdbs/{}_{}.pdb'.format(pdbID, chainID))
+                    else:  
+                        chain_pdb, protein_type, membrane_thickness = download_pdb('{}_{}'.format(pdbID.split('_')[0], chainID))
                     target_chains.append([pdbID.split('_')[0], chainID, chain_pdb, protein_type, membrane_thickness])
             else:
                 target_chains = None