diff --git a/src/pytom_tm/tmjob.py b/src/pytom_tm/tmjob.py
index 595067da..8805885a 100644
--- a/src/pytom_tm/tmjob.py
+++ b/src/pytom_tm/tmjob.py
@@ -177,9 +177,17 @@ def __init__(
         self.ctf_data = ctf_data
         self.whiten_spectrum = whiten_spectrum
         self.whitening_filter = self.output_dir.joinpath(f'{self.tomo_id}_whitening_filter.npy')
-        if self.whiten_spectrum and not self.whitening_filter.exists():
+        if self.whiten_spectrum:
             logging.info('Estimating whitening filter...')
-            weights = 1 / np.sqrt(power_spectrum_profile(read_mrc(self.tomogram)))
+            weights = 1 / np.sqrt(
+                power_spectrum_profile(
+                    read_mrc(self.tomogram)[
+                        self.search_origin[0]: self.search_origin[0] + self.search_size[0],
+                        self.search_origin[1]: self.search_origin[1] + self.search_size[1],
+                        self.search_origin[2]: self.search_origin[2] + self.search_size[2]
+                    ]
+                )
+            )
             weights /= weights.max()  # scale to 1
             np.save(self.whitening_filter, weights)
 
diff --git a/tests/test_tmjob.py b/tests/test_tmjob.py
index 0291c17f..8500630d 100644
--- a/tests/test_tmjob.py
+++ b/tests/test_tmjob.py
@@ -182,6 +182,18 @@ def test_tm_job_weighting_options(self):
         score, angle = job.start_job(0, return_volumes=True)
         self.assertEqual(score.shape, job.tomo_shape, msg='TMJob with only whitening filter failed')
 
+        # load the whitening filter from previous job to compare against
+        whitening_filter = np.load(TEST_WHITENING_FILTER)
+        job = TMJob('0', 10, TEST_TOMOGRAM, TEST_TEMPLATE, TEST_MASK, TEST_DATA_DIR,
+                    angle_increment='90.00', voxel_size=1., whiten_spectrum=True, search_y=[10, 90])
+        new_whitening_filter = np.load(TEST_WHITENING_FILTER)
+        self.assertNotEqual(whitening_filter.shape, new_whitening_filter.shape,
+                            msg='After reducing the search region along the largest dimension the whitening filter '
+                                'should have less sampling points')
+        self.assertEqual(new_whitening_filter.shape, (max(job.search_size) // 2 + 1, ),
+                         msg='The whitening filter does not have the expected size, it should be equal (x // 2) + 1, '
+                             'where x is the largest dimension of the search box.')
+
         # TMJob with none of these weighting options is tested in all other runs in this file.
 
     def test_custom_angular_search(self):