diff --git a/avogadro/qtgui/rwmolecule.h b/avogadro/qtgui/rwmolecule.h
index fad573e15..12dae4889 100644
--- a/avogadro/qtgui/rwmolecule.h
+++ b/avogadro/qtgui/rwmolecule.h
@@ -529,7 +529,28 @@ class AVOGADROQTGUI_EXPORT RWMolecule : public QObject
    * @param cartTol Cartesian tolerance for comparing atom positions.
    * @return True if the algorithm succeeded, and false if it failed.
    */
-  bool reduceCellToAsymmetricUnit(unsigned short hallNumber, double cartTol = 1e-5);
+  bool reduceCellToAsymmetricUnit(unsigned short hallNumber,
+                                  double cartTol = 1e-5);
+
+  /**
+   * Call this function when you wish to merge all undo commands.
+   * It turns on interactive mode to merge similar undo commands in a series
+   * (in order to save space), and it uses QUndoStack's beginMacro() to merge
+   * dissimilar undo commands together. You must call endMergeMode() to end
+   * the merging section (undo and redo are unavailable while merge mode is
+   * on).
+   * @param undoName The name of the undo command
+   */
+  void beginMergeMode(const QString& undoName = "Draw");
+
+  /**
+   * Call this function when you wish merge mode to end. This will turn off
+   * interactive mode, and it will call QUndoStack's endMacro(). All of the
+   * undo commands pushed between beginMergeMode() and endMergeMode() will be
+   * merged into one undo command. beginMergeMode() should have been called
+   * before this is called.
+   */
+  void endMergeMode();
 
   /**
    * @brief Begin or end an interactive edit.
@@ -771,6 +792,18 @@ inline std::pair<Index, Index> RWMolecule::bondPair(Index bondId) const
   return m_molecule.bondPair(bondId);
 }
 
+inline void RWMolecule::beginMergeMode(const QString& undoName)
+{
+  m_interactive = true;
+  m_undoStack.beginMacro(undoName);
+}
+
+inline void RWMolecule::endMergeMode()
+{
+  m_interactive = false;
+  m_undoStack.endMacro();
+}
+
 inline void RWMolecule::setInteractive(bool b)
 {
   m_interactive = b;
diff --git a/avogadro/qtplugins/editor/editor.cpp b/avogadro/qtplugins/editor/editor.cpp
index eecb171be..350ef9b1c 100644
--- a/avogadro/qtplugins/editor/editor.cpp
+++ b/avogadro/qtplugins/editor/editor.cpp
@@ -103,27 +103,28 @@ QWidget *Editor::toolWidget() const
 QUndoCommand *Editor::mousePressEvent(QMouseEvent *e)
 {
   clearKeyPressBuffer();
-  if (!m_renderer)
+  if (!m_renderer || !m_molecule)
     return NULL;
 
   updatePressedButtons(e, false);
   m_clickPosition = e->pos();
 
-  if (m_molecule) {
-    m_molecule->setInteractive(true);
-  }
-
   if (m_pressedButtons & Qt::LeftButton) {
     m_clickedObject = m_renderer->hit(e->pos().x(), e->pos().y());
 
     switch (m_clickedObject.type) {
     case Rendering::InvalidType:
+      m_molecule->beginMergeMode(tr("Draw Atom"));
       emptyLeftClick(e);
       return NULL;
     case Rendering::AtomType:
+      // We don't know yet if we are drawing a bond/atom or replacing an atom
+      // unfortunately...
+      m_molecule->beginMergeMode(tr("Draw"));
       atomLeftClick(e);
       return NULL;
     case Rendering::BondType:
+      m_molecule->beginMergeMode(tr("Change Bond Type"));
       bondLeftClick(e);
       return NULL;
     }
@@ -133,9 +134,11 @@ QUndoCommand *Editor::mousePressEvent(QMouseEvent *e)
 
     switch (m_clickedObject.type) {
     case Rendering::AtomType:
+      m_molecule->beginMergeMode(tr("Remove Atom"));
       atomRightClick(e);
       return NULL;
     case Rendering::BondType:
+      m_molecule->beginMergeMode(tr("Remove Bond"));
       bondRightClick(e);
       return NULL;
     default:
@@ -148,15 +151,11 @@ QUndoCommand *Editor::mousePressEvent(QMouseEvent *e)
 
 QUndoCommand *Editor::mouseReleaseEvent(QMouseEvent *e)
 {
-  if (!m_renderer)
+  if (!m_renderer || !m_molecule)
     return NULL;
 
   updatePressedButtons(e, true);
 
-  if (m_molecule) {
-    m_molecule->setInteractive(false);
-  }
-
   if (m_clickedObject.type == Rendering::InvalidType)
     return NULL;
 
@@ -165,6 +164,12 @@ QUndoCommand *Editor::mouseReleaseEvent(QMouseEvent *e)
   case Qt::RightButton:
     reset();
     e->accept();
+    m_molecule->endMergeMode();
+    // Let's cover all possible changes - the undo stack won't update
+    // without this
+    m_molecule->emitChanged(Molecule::Atoms | Molecule::Bonds |
+                            Molecule::Added | Molecule::Removed |
+                            Molecule::Modified);
     break;
   default:
     break;
@@ -599,7 +604,8 @@ void Editor::atomLeftDrag(QMouseEvent *e)
         RWBond bond = m_molecule->bond(newAtom, clickedAtom);
         if (bond.isValid()) {
           int bondOrder = expectedBondOrder(newAtom, clickedAtom);
-          bond.setOrder(bondOrder);
+          if (bondOrder != bond.order())
+            bond.setOrder(bondOrder);
 
           changes |= Molecule::Bonds | Molecule::Modified;
         }