diff --git a/benchmarks/benchmarks/analysis/rms.py b/benchmarks/benchmarks/analysis/rms.py
index 3d34f386c5a..bd1040cee04 100644
--- a/benchmarks/benchmarks/analysis/rms.py
+++ b/benchmarks/benchmarks/analysis/rms.py
@@ -34,9 +34,9 @@ def setup(self, num_atoms, weights, center, superposition):
             self.u.trajectory[-1]
             self.B = self.u.atoms.positions.copy()[:num_atoms]
         except:
-            self.A = self.u.atoms.coordinates().copy()[:num_atoms]
+            self.A = self.u.atoms.positions.copy()[:num_atoms]
             self.u.trajectory[-1]
-            self.B = self.u.atoms.coordinates().copy()[:num_atoms]
+            self.B = self.u.atoms.positions.copy()[:num_atoms]
 
     def time_rmsd(self, num_atoms, weights, center, superposition):
         """Benchmark rmsd function using a setup similar to
diff --git a/package/MDAnalysis/analysis/encore/covariance.py b/package/MDAnalysis/analysis/encore/covariance.py
index 352d934f9d5..0887749c010 100644
--- a/package/MDAnalysis/analysis/encore/covariance.py
+++ b/package/MDAnalysis/analysis/encore/covariance.py
@@ -215,7 +215,7 @@ def covariance_matrix(ensemble,
         # Select the same atoms in reference structure
         reference_atom_selection = reference.select_atoms(
             ensemble.get_atom_selection_string())
-        reference_coordinates = reference_atom_selection.atoms.coordinates()
+        reference_coordinates = reference_atom_selection.atoms.positions
 
         # Flatten reference coordinates
         reference_coordinates = reference_coordinates.flatten()
diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py
index b579c02bdbb..0e36272892f 100644
--- a/testsuite/MDAnalysisTests/analysis/test_encore.py
+++ b/testsuite/MDAnalysisTests/analysis/test_encore.py
@@ -395,6 +395,12 @@ def test_dres_error_estimation(self, ens1):
         assert stdev < stdev_upper_bound, "Unexpected standard deviation for" \
                                            " bootstrapped samples in Dim. reduction Ensemble imilarity"
 
+    def test_covariance_matrix(self, ens1, ens2):
+        covariance_of_matrix = encore.covariance_matrix(ensemble=ens1,
+                                                        reference=ens2)
+
+        assert covariance_of_matrix is np.zeros(len(ens1), 3)
+
 class TestEncoreClustering(object):
     @pytest.fixture(scope='class')
     def ens1_template(self):