From 1b7a0aed840d2bcaf223a87cb36b937d10f9e406 Mon Sep 17 00:00:00 2001
From: Han Zhu <zhu773@purdue.deu>
Date: Tue, 24 Sep 2024 18:06:53 -0400
Subject: [PATCH] update readme

---
 README.md  | 11 +++++++++--
 contour.py |  5 ++++-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index f04f0cb..3d66ab6 100644
--- a/README.md
+++ b/README.md
@@ -39,8 +39,15 @@ python main.py -F ./Class3D/job052/class1.mrc ./Class3D/job052/class2.mrc ./Clas
 -n: Number of intializations (Optional, 3 by default)
 ```
 
-## Example for Auto Contouring
+## Example for GMM Auto Contouring for Rough Masking
 
 ```
-python gmm_contour.py -i ./Class3D/job052/class1.mrc -o ./output_folder -p
+python contour.py -i ./Class3D/job052/class1.mrc -o ./output_folder -p
 ```
+
+
+## Example for CryoREAD Auto Refinement Masking
+
+```
+python contour.py -i ./Class3D/job052/class1.mrc -o ./output_folder -p
+```
\ No newline at end of file
diff --git a/contour.py b/contour.py
index a553814..767291c 100644
--- a/contour.py
+++ b/contour.py
@@ -28,7 +28,7 @@ def run_cryoREAD(mrc_path, output_folder, batch_size=4, gpu_id=None):
         f"--gpu={gpu_id}",
         f"--batch_size={batch_size}",
         f"--prediction_only",
-        f"--resolution=3",
+        f"--resolution=3.0",
         f"--output={output_folder}",
     ]
     os.system(" ".join(cmd))
@@ -255,6 +255,9 @@ def gmm_mask(input_map_path, output_folder, num_components=2, use_grad=False, n_
             batch_size=args.batch_size,
             gpu_id=args.gpu_id,
         )
+
+        final_protein_prob = os.path.join(args.output_folder, "2nd_stage_detection", "chain_protein_prob.mrc")
+
     else:
         revised_contour, mask_percent = gmm_mask(
             input_map_path=args.input_map_path,