diff --git a/prody/atomic/functions.py b/prody/atomic/functions.py
index 12964c96a..fb36c27dd 100644
--- a/prody/atomic/functions.py
+++ b/prody/atomic/functions.py
@@ -285,7 +285,7 @@ def sortAtoms(atoms, label, reverse=False):
     return AtomMap(ag, sort, acsi)
 
 
-def sliceAtoms(atoms, select):
+def sliceAtoms(atoms, select, allowSame=False):
     """Slice *atoms* using the selection defined by *select*.
 
     :arg atoms: atoms to be selected from
@@ -297,6 +297,8 @@ def sliceAtoms(atoms, select):
     """
 
     if atoms == select:
+        if allowSame:
+            return atoms._getSubset('all'), atoms.all
         raise ValueError('atoms and select arguments are the same')
 
     try:
diff --git a/prody/ensemble/ensemble.py b/prody/ensemble/ensemble.py
index 2e0c20361..9556ee1ba 100644
--- a/prody/ensemble/ensemble.py
+++ b/prody/ensemble/ensemble.py
@@ -217,7 +217,7 @@ def getAtoms(self, selected=True):
             return self._atoms
         return self._atoms[self._indices]
 
-    def setAtoms(self, atoms):
+    def setAtoms(self, atoms, allowSame=False):
         """Set *atoms* or specify a selection of atoms to be considered in
         calculations and coordinate requests.  When a selection is set,
         corresponding subset of coordinates will be considered in, for
@@ -238,7 +238,7 @@ def setAtoms(self, atoms):
 
         n_atoms = self._n_atoms
         if n_atoms:
-            if atoms.numAtoms() > n_atoms:
+            if atoms.numAtoms() > n_atoms and atoms.ca.numAtoms() > n_atoms:
                 raise ValueError('atoms must be same size or smaller than '
                                 'the ensemble')
 
@@ -261,11 +261,19 @@ def setAtoms(self, atoms):
                     ag = atoms.getAtomGroup()
                 except AttributeError:
                     ag = atoms
-                if ag.numAtoms() != n_atoms:
+                try:
+                    self_ag = self._atoms.getAtomGroup()
+                except AttributeError:
+                    self_ag = self._atoms
+                try:
+                    self_ag_n_atoms = self_ag.numAtoms()
+                except AttributeError:
+                    self_ag_n_atoms = 0
+                if ag.numAtoms() != n_atoms and ag.numAtoms() != self_ag_n_atoms and self_ag_n_atoms != 0:
                     raise ValueError('size mismatch between this ensemble ({0} atoms) and atoms ({1} atoms)'
                                     .format(n_atoms, ag.numAtoms()))
                 self._atoms = ag
-                self._indices, _ = sliceAtoms(self._atoms, atoms)
+                self._indices, _ = sliceAtoms(self._atoms, atoms, allowSame=allowSame)
                 
         else: # if assigning atoms to a new ensemble
             self._n_atoms = atoms.numAtoms()
@@ -294,12 +302,32 @@ def getCoords(self, selected=True):
             return None
         if self._indices is None or not selected:
             return self._coords.copy()
-        return self._coords[self._indices].copy()
+        
+        selids = self._indices
+        if self.hasSelectionIssue():
+            selids = self.getIndices(calphas=True)
+        return self._coords[selids].copy()
 
-    def getIndices(self):
+    def getIndices(self, calphas=False):
         """Returns a copy of indices of selected columns"""
 
+        if calphas:
+            return array([list(self._atoms.ca.getIndices()).index(idx) 
+                          for idx in self._indices])
         return copy(self._indices)
+    
+    def hasSelectionIssue(self):
+        if self._atoms is None or self._atoms.ca is None:
+            return False
+        
+        selids = self._indices
+        if selids is None:
+            return False
+
+        if (selids.max() > self._coords.shape[0] 
+            and set(selids).issubset(set(self._atoms.ca.getIndices()))):
+            return True
+        return False        
 
     def setIndices(self, value):
         if not isListLike(value):
@@ -359,10 +387,17 @@ def getWeights(self, selected=True):
             return None
         if self._indices is None or not selected:
             return self._weights.copy()
+        
+        
+        if self.hasSelectionIssue():
+            selids = self.getIndices(calphas=True)
+        else:
+            selids = self._indices
+            
         if self._weights.ndim == 2:
-            return self._weights[self._indices].copy()
+            return self._weights[selids].copy()
         else:
-            return self._weights[:, self._indices].copy()
+            return self._weights[:, selids].copy()
 
     def _getWeights(self, selected=True):
 
diff --git a/prody/ensemble/functions.py b/prody/ensemble/functions.py
index cbe142310..f3f108568 100644
--- a/prody/ensemble/functions.py
+++ b/prody/ensemble/functions.py
@@ -215,7 +215,7 @@ def loadEnsemble(filename, **kwargs):
                 data[key] = arr
     else:
         atoms = None
-    ensemble.setAtoms(atoms)
+    ensemble.setAtoms(atoms, allowSame=True)
 
     if '_indices' in attr_dict:
         indices = attr_dict['_indices']
diff --git a/prody/ensemble/pdbensemble.py b/prody/ensemble/pdbensemble.py
index a141b77a8..4322de31b 100644
--- a/prody/ensemble/pdbensemble.py
+++ b/prody/ensemble/pdbensemble.py
@@ -459,6 +459,9 @@ def getMSA(self, indices=None, selected=True):
         
         atom_indices = self._indices if selected else slice(None, None, None)
         indices = indices if indices is not None else slice(None, None, None)
+
+        if self.hasSelectionIssue():
+            atom_indices = self.getIndices(calphas=True)
         
         return self._msa[indices, atom_indices]
 
@@ -491,6 +494,8 @@ def getCoordsets(self, indices=None, selected=True):
                 confs[i, which] = coords[which]
         else:
             selids = self._indices
+            if self.hasSelectionIssue():
+                selids = self.getIndices(calphas=True)
             coords = coords[selids]
             confs = self._confs[indices, selids].copy()
             for i, w in enumerate(self._weights[indices]):