diff --git a/src/biotite/structure/__init__.py b/src/biotite/structure/__init__.py
index 3dd06a1dd..3c9f85d88 100644
--- a/src/biotite/structure/__init__.py
+++ b/src/biotite/structure/__init__.py
@@ -15,7 +15,7 @@
 An `Atom` contains data for a single atom, it stores the annotations as
 scalar values and the coordinates as length 3 `ndarray`.
 An `AtomArray` stores data for an entire structure model containing *n*
-atoms. Therefore the annotations are represented as `ndarray`s of
+atoms. Therefore the annotations are represented as `ndarray` objects of
 length *n*, so called annotation arrays. The coordinates are a (n x 3)
 `ndarray`.
 `AtomArrayStack` stores data for *m* models. Each `AtomArray` in
diff --git a/src/biotite/structure/atoms.py b/src/biotite/structure/atoms.py
index 0f91a3e7c..3b0b7b1d8 100644
--- a/src/biotite/structure/atoms.py
+++ b/src/biotite/structure/atoms.py
@@ -333,8 +333,10 @@ def __dir__(self):
         attr = super().__dir__()
         attr.append("coord")
         attr.append("bonds")
+        attr.append("box")
         for name in self._annot.keys():
             attr.append(name)
+        return attr
     
     def __eq__(self, item):
         """
@@ -819,7 +821,7 @@ def __init__(self, depth, length):
         if depth == None or length == None:
             self._coord = None
         else:
-            self._coord = np.zeros((depth, length, 3), dtype=float)
+            self._coord = np.full((depth, length, 3), np.nan, dtype=float)
     
     def get_array(self, index):
         """