diff --git a/src/mattersim/datasets/utils/convertor.py b/src/mattersim/datasets/utils/convertor.py
index d01776f..dc36687 100644
--- a/src/mattersim/datasets/utils/convertor.py
+++ b/src/mattersim/datasets/utils/convertor.py
@@ -114,36 +114,13 @@ def get_fixed_radius_bonding(
     Returns:
         center_indices, neighbor_indices, images, distances
     """
-    if isinstance(structure, Atoms):
-        pbc_ = np.array(structure.pbc, dtype=int)
-        if np.all(pbc_ < 0.01) or not pbc:
-            min_x = np.min(structure.positions[:, 0])
-            min_y = np.min(structure.positions[:, 1])
-            min_z = np.min(structure.positions[:, 2])
-            max_x = np.max(structure.positions[:, 0])
-            max_y = np.max(structure.positions[:, 1])
-            max_z = np.max(structure.positions[:, 2])
-            x_len = max((max_x - min_x) * 10, 1000)
-            y_len = max((max_y - min_y) * 10, 1000)
-            z_len = max((max_z - min_z) * 10, 1000)
-            lattice_matrix = np.array(
-                [[x_len, 0.0, 0.0], [0.0, y_len, 0.0], [0.0, 0.0, z_len]],
-                dtype=float,
-            )
-            pbc_ = np.array([1, 1, 1], dtype=int)
-            warnings.warn("No PBC detected, using a large supercell", UserWarning)
-        else:
-            if np.all(structure.cell < 1e-5):
-                raise ValueError("Cell vectors are too small")
-            lattice_matrix = np.ascontiguousarray(
-                structure.cell[:], dtype=float
-            )  # noqa: E501
+    pbc_ = np.array(structure.pbc, dtype=int)
 
-        cart_coords = np.ascontiguousarray(
-            np.array(structure.positions), dtype=float
-        )  # noqa: E501
-    else:
-        raise ValueError("structure type not supported")
+    lattice_matrix = np.ascontiguousarray(structure.cell[:], dtype=float)  # noqa: E501
+
+    cart_coords = np.ascontiguousarray(
+        np.array(structure.positions), dtype=float
+    )  # noqa: E501
     r = float(cutoff)
 
     (
@@ -208,6 +185,32 @@ def convert(
             pbc: bool, whether to use periodic boundary condition, default True
         """
         # normalize the structure
+        if isinstance(atoms, Atoms):
+            pbc_ = np.array(atoms.pbc, dtype=int)
+            if np.all(pbc_ < 0.01) or not pbc:
+                min_x = np.min(atoms.positions[:, 0])
+                min_y = np.min(atoms.positions[:, 1])
+                min_z = np.min(atoms.positions[:, 2])
+                max_x = np.max(atoms.positions[:, 0])
+                max_y = np.max(atoms.positions[:, 1])
+                max_z = np.max(atoms.positions[:, 2])
+                x_len = max((max_x - min_x) * 10, 1000)
+                y_len = max((max_y - min_y) * 10, 1000)
+                z_len = max((max_z - min_z) * 10, 1000)
+                lattice_matrix = np.array(
+                    [[x_len, 0.0, 0.0], [0.0, y_len, 0.0], [0.0, 0.0, z_len]],
+                    dtype=float,
+                )
+                pbc_ = np.array([1, 1, 1], dtype=int)
+                warnings.warn("No PBC detected, using a large supercell", UserWarning)
+                atoms.set_cell(lattice_matrix)
+                atoms.set_pbc(pbc_)
+            else:
+                if np.all(atoms.cell < 1e-5):
+                    raise ValueError("Cell vectors are too small")
+        else:
+            raise ValueError("structure type not supported")
+
         scaled_pos = atoms.get_scaled_positions()
         scaled_pos = np.mod(scaled_pos, 1)
         atoms.set_scaled_positions(scaled_pos)