diff --git a/bin/partial_noise_reconstruct.py b/bin/partial_noise_reconstruct.py
index cef96a7..d3b6f7f 100644
--- a/bin/partial_noise_reconstruct.py
+++ b/bin/partial_noise_reconstruct.py
@@ -54,8 +54,11 @@ def load_dataset(pdb_files: Collection[str], model_dir: Path):
 
 
 def build_parser():
-    parser = argparse.ArgumentParser(usage=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser = argparse.ArgumentParser(
+        usage=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
     parser.add_argument("pdb_files", nargs="+", help="PDB files to reconstruct")
+    parser.add_argument("output_json", type=str, help="Output JSON file")
     parser.add_argument(
         "-t",
         "--timesteps",
@@ -75,7 +78,7 @@ def get_reconstruction_error(
     timesteps: int = 800,
     model: str = "wukevin/foldingdiff_cath",
     device: torch.device = torch.device("cuda:1"),
-):
+) -> np.ndarray:
     """Get the reconstruction error for a set of PDB files"""
     if utils.is_huggingface_hub_id(model):
         logging.info(f"Detected huggingface repo ID {model}")
@@ -102,6 +105,7 @@ def get_reconstruction_error(
     logging.info(
         f"Reconstuction scores from t={timesteps}: {(np.min(scores_wrt_coords), np.max(scores_wrt_coords))}"
     )
+    return scores_wrt_coords
 
 
 def main():
@@ -109,12 +113,16 @@ def main():
     parser = build_parser()
     args = parser.parse_args()
 
-    get_reconstruction_error(
+    scores = get_reconstruction_error(
         args.pdb_files,
         timesteps=args.timesteps,
         model=args.model,
         device=torch.device(f"cuda:{args.device}"),
     )
+    
+    scores_dict = {pdb: score for pdb, score in zip(args.pdb_files, scores)}
+    with open(args.output_json, "w") as sink:
+        json.dump(scores_dict, sink, indent=4)
 
 
 if __name__ == "__main__":