diff --git a/.idea/ruff.xml b/.idea/ruff.xml
index d2889cf568b0b14ece74f0674b0336ffad272b2d..d3a43c2692798cf84ac6aa5d6f9894a6cddb096d 100644
--- a/.idea/ruff.xml
+++ b/.idea/ruff.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
   <component name="RuffConfigService">
-    <option name="projectRuffExecutablePath" value="$USER_HOME$/anaconda3/bin/ruff" />
+    <option name="projectRuffExecutablePath" value="$USER_HOME$/anaconda3/envs/catm/bin/ruff" />
   </component>
 </project>
\ No newline at end of file
diff --git a/README.md b/README.md
index 4ea2e64a8ded5f0f735811dfc03f273ce0599276..4913d0c66c48add9513961cddb75dc590c383613 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ python version at least 3.5 is required, create a separated environment if you w
 1.  Creat a new vitual enviroment (optional)
 
 ```
-conda create -n CATM python 
+conda create -n catm python 
 ```
 2. Download the package from gitlab and change directory to the CATM folder
 ```
@@ -23,7 +23,7 @@ git clone https://git.biohpc.swmed.edu/s194231/cryo-catm.git
 cd cryo-catm
 ```
 
-2.  Install the package
+2.  Install the package, if you want to build your own code activiely, add -dev option
 
 ```
 pip install .
@@ -33,7 +33,7 @@ pip install .
 
 ```
 cd test
-CATM #run the main program
+catm #run the main program
 ```
 
 
diff --git a/src/catm.py b/src/catm.py
index 0386331cc5c911be20562807eb43c6cc47d4aa60..642ec8c921ca0e1f55fef83fb8802e8d84bc8c3b 100644
--- a/src/catm.py
+++ b/src/catm.py
@@ -45,7 +45,7 @@ def main():
     user_inputs = parse_input()
     if hasattr(config, "testTM"):  # this will run only the global TM
         if config.testTM:
-            print("Running general template matching!")
+            print("Running regular template matching!")
             matcher = TemplateMatcherGeneral(user_inputs)
             matcher.run_multiprocessing()
             end_time = time.time()
@@ -61,7 +61,7 @@ def main():
         obj_xml = matcher.run_multiprocessing()
         print("Template matching finished, saving results")
     else:
-        print("Bypassing template matching")
+        print("Bypassed template matching")
         # for debugging, read the xml file
         from lxml.etree import XMLParser, parse
 
diff --git a/src/global_template_matching.py b/src/global_template_matching.py
index 40d3eb06336398862db645c5d11094e81754e5a7..954640354e99efedab92dc0ae74e01ce8b2b2b3f 100644
--- a/src/global_template_matching.py
+++ b/src/global_template_matching.py
@@ -65,7 +65,6 @@ class TemplateMatcherGeneral:
             indices = list(range(len(self.global_angles)))
             results = pool.map(self.match_worker, indices)
             # Process results in order
-        print(len(results))
         print("Template matching is done, sorting the results!")
         # scores, rot_new, coord_new, model = [], [], [], []
         # Initialize the arrays
@@ -86,7 +85,6 @@ class TemplateMatcherGeneral:
             # Assign the temporary array to rot_save where the mask is True
             rot_save[mask] = temp_array[mask]
         # Verify the result for one element
-        print(rot_save[0, 0, 0])  # Example verification
         """        rot_save = np.empty(self.dims, dtype=object)
         ccc_save = np.zeros(self.dims)
         for cur_ccc, cur_rot in results:
diff --git a/src/template_matching.py b/src/template_matching.py
index 108c6affdbf02f9a58ac33e070e7fcd263a22c3e..4913e51001749aa58fa033747a0a2254b057d47d 100644
--- a/src/template_matching.py
+++ b/src/template_matching.py
@@ -54,6 +54,7 @@ class TemplateMatcher:
             ctf_volumes = prepare_ctf_volumes(self.ctf, self.templates)
         else:
             ctf_volumes = []
+        #print("Working on subtomogram " + str(index))
         score, rots, coords, models = self.template_match(
             subtomo, angles, self.coords[index], ctf_volumes
         )
@@ -212,7 +213,6 @@ class TemplateMatcher:
                     mask = apply_wedge(mask, self.missing_wedge)
                     mask[mask < 0.5] = 0  # the mask should be binary
                     mask[mask >= 0.5] = 1
-
                 cur_ccc.append(calculate_correlation(subtomo[temp], template_rot, mask))
             ccc_save, rot_save, coor_save = self.get_best_match(
                 cur_ccc,