diff --git a/alphapulldown/create_individual_features.py b/alphapulldown/create_individual_features.py
index 53d8bf11..32abf5fb 100644
--- a/alphapulldown/create_individual_features.py
+++ b/alphapulldown/create_individual_features.py
@@ -32,7 +32,7 @@
 flags = run_af.flags
 
 # All flags
-flags.DEFINE_bool("use_mmseqs2", False, "Use mmseqs2 remotely or not. Default is False")
+flags.DEFINE_string("use_mmseqs2", "false", "Use mmseqs2 remotely or not. 'true' or 'false', default is 'false'")
 flags.DEFINE_bool("save_msa_files", False, "Save MSA output or not")
 flags.DEFINE_bool("skip_existing", False, "Skip existing monomer feature pickles or not")
 flags.DEFINE_string("new_uniclust_dir", None, "Directory where new version of uniclust is stored")
@@ -52,6 +52,7 @@
 flags.DEFINE_float("plddt_threshold", 0, "Threshold for pLDDT score (default: 0)")
 
 FLAGS = flags.FLAGS
+
 MAX_TEMPLATE_HITS = 20
 
 flags_dict = FLAGS.flag_values_dict()
@@ -195,6 +196,7 @@ def create_and_save_monomer_objects(monomer, pipeline):
     with output_meta_file(metadata_output_path) as meta_data_outfile:
         save_meta_data(flags_dict, meta_data_outfile)
 
+    FLAGS.use_mmseqs2 = FLAGS.use_mmseqs2.lower() == 'true'
     # Create features
     if FLAGS.use_mmseqs2:
         logging.info("Running MMseqs2 for feature generation...")