diff --git a/barrOs_library.py b/barrOs_library.py
index da22e1dc2dedd46c96820306d96ef4155c56e7b5..b92733eb8eeca692f9a1037211fed08e3c9c768e 100644
--- a/barrOs_library.py
+++ b/barrOs_library.py
@@ -349,7 +349,7 @@ def get_all_pdbIDs(input_files, input_types):
             pdb_file = input_string
             pdbIDs.append(pdb_file)
         elif input_types[i] == 'pdb_folder':
-            pdb_files = ['{}/{}'.format(input_string, f) for f in os.listdir(input_string) if f.endswith('.pdb')]
+            pdb_files = ['{}/{}'.format(input_string, f) for f in os.listdir(input_string) if f.endswith('.pdb') and 'barrelOnly' not in f and 'moved_to_reference' not in f]
             pdbIDs += pdb_files
         elif input_types[i] == 'pdbID':
             pdbIDs.append(input_string)