Issue MDAnalysis#3467

pranjii · Dec 8, 2021 · 5d1f343 · 5d1f343
1 parent 5bf6359
commit 5d1f343
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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()