diff --git a/avogadro/qtgui/rwmolecule.cpp b/avogadro/qtgui/rwmolecule.cpp
index 42a73bc183..62c240f26e 100644
--- a/avogadro/qtgui/rwmolecule.cpp
+++ b/avogadro/qtgui/rwmolecule.cpp
@@ -182,10 +182,13 @@ bool RWMolecule::setAtomPosition3d(Index atomId, const Vector3& pos,
   return true;
 }
 
-void RWMolecule::setAtomSelected(Index atomId, bool selected)
+void RWMolecule::setAtomSelected(Index atomId, bool selected, const QString& undoText)
 {
-  // FIXME: Add in an implementation (and use it from the selection tool).
-  m_molecule.setAtomSelected(atomId, selected);
+  auto* comm = new ModifySelectionCommand(*this, atomId, selected);
+  comm->setText(undoText);
+  comm->setCanMerge(true);
+  m_undoStack.push(comm);
+//  m_molecule.setAtomSelected(atomId, selected);
 }
 
 bool RWMolecule::atomSelected(Index atomId) const
diff --git a/avogadro/qtgui/rwmolecule.h b/avogadro/qtgui/rwmolecule.h
index 82da454fe3..4911652d6f 100644
--- a/avogadro/qtgui/rwmolecule.h
+++ b/avogadro/qtgui/rwmolecule.h
@@ -203,9 +203,6 @@ class AVOGADROQTGUI_EXPORT RWMolecule : public QObject
    */
   Vector3 atomPosition3d(Index atomId) const;
 
-  std::string label(Index atomId) const;
-  bool setLabel(Index atomId, const std::string& label,
-                const QString& undoText = QStringLiteral("Change Atom Label"));
   /**
    * Replace the current array of 3D atomic coordinates.
    * @param pos The new coordinate array. Must be of length atomCount().
@@ -214,7 +211,7 @@ class AVOGADROQTGUI_EXPORT RWMolecule : public QObject
    */
   bool setAtomPositions3d(
     const Core::Array<Vector3>& pos,
-    const QString& undoText = QStringLiteral("Change Atom Positions"));
+    const QString& undoText = tr("Change Atom Positions"));
 
   /**
    * Set the 3D position of a single atom.
@@ -223,14 +220,18 @@ class AVOGADROQTGUI_EXPORT RWMolecule : public QObject
    * @param undoText The undo text to be displayed for undo commands.
    * @return True on success, false otherwise.
    */
-  bool setAtomPosition3d(
-    Index atomId, const Vector3& pos,
-    const QString& undoText = QStringLiteral("Change Atom Position"));
+  bool setAtomPosition3d(Index atomId, const Vector3& pos,
+                         const QString& undoText = tr("Change Atom Position"));
+
+  std::string label(Index atomId) const;
+  bool setLabel(Index atomId, const std::string& label,
+                const QString& undoText = tr("Change Atom Label"));
 
   /**
    * Set whether the specified atom is selected or not.
    */
-  void setAtomSelected(Index atomId, bool selected);
+  void setAtomSelected(Index atomId, bool selected,
+                       const QString& undoText = tr("Change Selection"));
 
   /**
    * Query whether the supplied atom index has been selected.
@@ -834,9 +835,8 @@ inline Core::Array<RWMolecule::BondType> RWMolecule::bonds(
   auto atomBonds = m_molecule.bonds(atomId);
   Core::Array<RWMolecule::BondType> result;
   for (Index i = 0; i < atomBonds.size(); ++i) {
-    result.push_back(BondType(
-      const_cast<RWMolecule *>(this), atomBonds[i].index()
-    ));
+    result.push_back(
+      BondType(const_cast<RWMolecule*>(this), atomBonds[i].index()));
   }
   return result;
 }
diff --git a/avogadro/qtgui/rwmolecule_undo.h b/avogadro/qtgui/rwmolecule_undo.h
index 2076806671..f6c1ca1cd6 100644
--- a/avogadro/qtgui/rwmolecule_undo.h
+++ b/avogadro/qtgui/rwmolecule_undo.h
@@ -6,6 +6,7 @@
 #define AVOGADRO_QTGUI_RWMOLECULE_UNDO_H
 
 #include "rwmolecule.h"
+#include <QtCore/QDebug>
 #include <QtWidgets/QUndoCommand>
 #include <cassert>
 
@@ -28,7 +29,8 @@ class RWMolecule::UndoCommand : public QUndoCommand
 public:
   UndoCommand(RWMolecule& m)
     : QUndoCommand(tr("Modify Molecule")), m_mol(m), m_molecule(m.m_molecule)
-  {}
+  {
+  }
 
 protected:
   Array<Vector3>& positions3d() { return m_molecule.atomPositions3d(); }
@@ -45,7 +47,9 @@ enum MergeIds
   SetPositions3dMergeId = 0,
   SetPosition3dMergeId,
   SetForceVectorMergeId,
-  SetBondOrderMergeId
+  SetBondOrderMergeId,
+  ModifySelectionMergeId,
+  ModifyColorsMergeId
 };
 
 // Base class for undo commands that can be merged together, overriding the
@@ -120,7 +124,8 @@ class RemoveAtomCommand : public RWMolecule::UndoCommand
                     const Vector3& pos)
     : UndoCommand(m), m_atomId(atomId), m_atomUid(uid), m_atomicNumber(aN),
       m_position3d(pos)
-  {}
+  {
+  }
 
   void redo() override
   {
@@ -156,7 +161,8 @@ class SetAtomicNumbersCommand : public RWMolecule::UndoCommand
                           const Core::Array<unsigned char>& newAtomicNumbers)
     : UndoCommand(m), m_oldAtomicNumbers(oldAtomicNumbers),
       m_newAtomicNumbers(newAtomicNumbers)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.setAtomicNumbers(m_newAtomicNumbers); }
 
@@ -177,7 +183,8 @@ class SetAtomicNumberCommand : public RWMolecule::UndoCommand
                          unsigned char newAtomicNumber)
     : UndoCommand(m), m_atomId(atomId), m_oldAtomicNumber(oldAtomicNumber),
       m_newAtomicNumber(newAtomicNumber)
-  {}
+  {
+  }
 
   void redo() override
   {
@@ -203,7 +210,8 @@ class SetPositions3dCommand : public MergeUndoCommand<SetPositions3dMergeId>
                         const Core::Array<Vector3>& newPositions3d)
     : MergeUndoCommand<SetPositions3dMergeId>(m),
       m_oldPositions3d(oldPositions3d), m_newPositions3d(newPositions3d)
-  {}
+  {
+  }
 
   void redo() override { positions3d() = m_newPositions3d; }
 
@@ -235,7 +243,8 @@ class SetPosition3dCommand : public MergeUndoCommand<SetPosition3dMergeId>
                        const Vector3& newPosition3d)
     : MergeUndoCommand<SetPosition3dMergeId>(m), m_atomIds(1, atomId),
       m_oldPosition3ds(1, oldPosition3d), m_newPosition3ds(1, newPosition3d)
-  {}
+  {
+  }
 
   void redo() override
   {
@@ -302,7 +311,8 @@ class SetAtomHybridizationCommand : public RWMolecule::UndoCommand
                               AtomHybridization newHybridization)
     : UndoCommand(m), m_atomId(atomId), m_oldHybridization(oldHybridization),
       m_newHybridization(newHybridization)
-  {}
+  {
+  }
 
   void redo() override
   {
@@ -328,7 +338,8 @@ class SetAtomFormalChargeCommand : public RWMolecule::UndoCommand
                              signed char newCharge)
     : UndoCommand(m), m_atomId(atomId), m_oldCharge(oldCharge),
       m_newCharge(newCharge)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.setFormalCharge(m_atomId, m_newCharge); }
 
@@ -348,7 +359,8 @@ class SetAtomColorCommand : public RWMolecule::UndoCommand
                       Vector3ub newColor)
     : UndoCommand(m), m_atomId(atomId), m_oldColor(oldColor),
       m_newColor(newColor)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.setColor(m_atomId, m_newColor); }
 
@@ -365,7 +377,8 @@ class SetLayerCommand : public RWMolecule::UndoCommand
   SetLayerCommand(RWMolecule& m, Index atomId, size_t oldLayer, size_t newLayer)
     : UndoCommand(m), m_atomId(atomId), m_oldLayer(oldLayer),
       m_newLayer(newLayer)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.setLayer(m_atomId, m_newLayer); }
 
@@ -385,7 +398,8 @@ class AddBondCommand : public RWMolecule::UndoCommand
                  Index uid)
     : UndoCommand(m), m_bondOrder(order), m_bondPair(bondPair),
       m_bondId(bondId), m_bondUid(uid)
-  {}
+  {
+  }
 
   void redo() override
   {
@@ -415,13 +429,15 @@ class RemoveBondCommand : public RWMolecule::UndoCommand
                     unsigned char bondOrder)
     : UndoCommand(m), m_bondId(bondId), m_bondUid(bondUid),
       m_bondPair(bondPair), m_bondOrder(bondOrder)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.removeBond(m_bondId); }
 
   void undo() override
   {
-    m_molecule.addBond(m_bondPair.first, m_bondPair.second, m_bondOrder, m_bondUid);
+    m_molecule.addBond(m_bondPair.first, m_bondPair.second, m_bondOrder,
+                       m_bondUid);
     Index movedId = m_molecule.bondCount() - 1;
     m_molecule.swapBond(m_bondId, movedId);
   }
@@ -439,7 +455,8 @@ class SetBondOrdersCommand : public RWMolecule::UndoCommand
                        const Array<unsigned char>& newBondOrders)
     : UndoCommand(m), m_oldBondOrders(oldBondOrders),
       m_newBondOrders(newBondOrders)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.setBondOrders(m_newBondOrders); }
 
@@ -459,7 +476,8 @@ class SetBondOrderCommand : public MergeUndoCommand<SetBondOrderMergeId>
                       unsigned char newBondOrder)
     : MergeUndoCommand<SetBondOrderMergeId>(m), m_bondId(bondId),
       m_oldBondOrder(oldBondOrder), m_newBondOrder(newBondOrder)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.setBondOrder(m_bondId, m_newBondOrder); }
 
@@ -490,7 +508,8 @@ class SetBondPairsCommand : public RWMolecule::UndoCommand
                       const Array<std::pair<Index, Index>>& oldBondPairs,
                       const Array<std::pair<Index, Index>>& newBondPairs)
     : UndoCommand(m), m_oldBondPairs(oldBondPairs), m_newBondPairs(newBondPairs)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.setBondPairs(m_newBondPairs); }
 
@@ -511,7 +530,8 @@ class SetBondPairCommand : public RWMolecule::UndoCommand
                      const std::pair<Index, Index>& newBondPair)
     : UndoCommand(m), m_bondId(bondId), m_oldBondPair(oldBondPair),
       m_newBondPair(newBondPair)
-  {}
+  {
+  }
 
   void redo() override { m_molecule.setBondPair(m_bondId, m_newBondPair); }
 
@@ -527,7 +547,8 @@ class AddUnitCellCommand : public RWMolecule::UndoCommand
 public:
   AddUnitCellCommand(RWMolecule& m, const UnitCell& newUnitCell)
     : UndoCommand(m), m_newUnitCell(newUnitCell)
-  {}
+  {
+  }
 
   void redo() override
   {
@@ -546,7 +567,8 @@ class RemoveUnitCellCommand : public RWMolecule::UndoCommand
 public:
   RemoveUnitCellCommand(RWMolecule& m, const UnitCell& oldUnitCell)
     : UndoCommand(m), m_oldUnitCell(oldUnitCell)
-  {}
+  {
+  }
 
   void redo() override { m_mol.molecule().setUnitCell(nullptr); }
 
@@ -567,7 +589,8 @@ class ModifyMoleculeCommand : public RWMolecule::UndoCommand
   ModifyMoleculeCommand(RWMolecule& m, const Molecule& oldMolecule,
                         const Molecule& newMolecule)
     : UndoCommand(m), m_oldMolecule(oldMolecule), m_newMolecule(newMolecule)
-  {}
+  {
+  }
 
   void redo() override { m_mol.molecule() = m_newMolecule; }
 
@@ -588,7 +611,8 @@ class SetForceVectorCommand : public MergeUndoCommand<SetForceVectorMergeId>
                         const Vector3& newForceVector)
     : MergeUndoCommand<SetForceVectorMergeId>(m), m_atomIds(1, atomId),
       m_oldForceVectors(1, oldForceVector), m_newForceVectors(1, newForceVector)
-  {}
+  {
+  }
 
   void redo() override
   {
@@ -662,6 +686,124 @@ class ModifyLabelCommand : public RWMolecule::UndoCommand
 };
 } // namespace
 
+namespace {
+class ModifySelectionCommand : public MergeUndoCommand<ModifySelectionMergeId>
+{
+  std::vector<bool> m_newSelectedAtoms;
+  std::vector<bool> m_oldSelectedAtoms;
+
+public:
+  ModifySelectionCommand(RWMolecule& m, Index atomId, bool selected)
+    : MergeUndoCommand<ModifySelectionMergeId>(m)
+  {
+    Index atomCount = m_mol.molecule().atomCount();
+    m_oldSelectedAtoms.resize(atomCount);
+    m_newSelectedAtoms.resize(atomCount);
+
+    for (Index i = 0; i < atomCount; ++i) {
+      m_oldSelectedAtoms[i] = m_molecule.atomSelected(i);
+      m_newSelectedAtoms[i] = m_molecule.atomSelected(i);
+    }
+
+    m_newSelectedAtoms[atomId] = selected;
+  }
+
+  void redo() override
+  {
+    Index atomCount = m_mol.molecule().atomCount();
+    for (Index i = 0; i < atomCount; ++i)
+      m_mol.molecule().setAtomSelected(i, m_newSelectedAtoms[i]);
+  }
+
+  void undo() override
+  {
+    Index atomCount = m_mol.molecule().atomCount();
+    for (Index i = 0; i < atomCount; ++i)
+      m_mol.molecule().setAtomSelected(i, m_oldSelectedAtoms[i]);
+  }
+
+  bool mergeWith(const QUndoCommand* other) override
+  {
+    const ModifySelectionCommand* o =
+      dynamic_cast<const ModifySelectionCommand*>(other);
+    if (!o)
+      return false;
+
+    // check if the atom count matches
+    Index numAtoms = m_oldSelectedAtoms.size();
+
+    if (numAtoms != o->m_oldSelectedAtoms.size() ||
+        numAtoms != o->m_newSelectedAtoms.size())
+      return false;
+
+    // merge these, by grabbing the new selected atoms
+    m_newSelectedAtoms = o->m_newSelectedAtoms;
+    return true;
+  }
+};
+} // namespace
+
+/*
+namespace {
+class ModifyColorCommand : public MergeUndoCommand<ModifyColorMergeId>
+{
+  Array<Vector3ub> m_newSelectedAtoms;
+  Array<Vector3ub> m_oldSelectedAtoms;
+
+public:
+  ModifySelectionCommand(RWMolecule& m, Index atomId, bool selected)
+    : MergeUndoCommand<ModifySelectionMergeId>(m)
+  {
+    Index atomCount = m_mol.molecule().atomCount();
+    m_oldSelectedAtoms.reserve(atomCount);
+    m_newSelectedAtoms.reserve(atomCount);
+
+    for (Index i = 0; i < atomCount; ++i) {
+      m_oldSelectedAtoms[i] = m_molecule.atomSelected(i);
+      m_newSelectedAtoms[i] = m_molecule.atomSelected(i);
+    }
+
+    m_newSelectedAtoms[atomId] = selected;
+  }
+
+  void redo() override
+  {
+    Index atomCount = m_mol.molecule().atomCount();
+    for (Index i = 0; i < atomCount; ++i)
+      m_mol.molecule().setAtomSelected(i, m_newSelectedAtoms[i]);
+  }
+
+  void undo() override
+  {
+    Index atomCount = m_mol.molecule().atomCount();
+    for (Index i = 0; i < atomCount; ++i)
+      m_mol.molecule().setAtomSelected(i, m_oldSelectedAtoms[i]);
+  }
+
+  bool mergeWith(const QUndoCommand* other) override
+  {
+    const ModifySelectionCommand* o =
+      dynamic_cast<const ModifySelectionCommand*>(other);
+    if (o) {
+      // check if the atom count matches
+      Index numAtoms = m_oldSelectedAtoms.size();
+      if (numAtoms != o->m_oldSelectedAtoms.size() ||
+          numAtoms != o->m_newSelectedAtoms.size()) {
+        return false;
+      }
+
+      // merge these, by grabbing the new selected atoms
+      for (Index i = 0; i < numAtoms; ++i)
+        m_newSelectedAtoms[i] = o->m_newSelectedAtoms[i];
+
+      return true;
+    }
+    return false;
+  }
+};
+} // namespace
+*/
+
 } // namespace QtGui
 } // namespace Avogadro
 #endif
diff --git a/avogadro/qtplugins/propertytables/propertyview.cpp b/avogadro/qtplugins/propertytables/propertyview.cpp
index a1ea07af52..88900dab54 100644
--- a/avogadro/qtplugins/propertytables/propertyview.cpp
+++ b/avogadro/qtplugins/propertytables/propertyview.cpp
@@ -78,7 +78,7 @@ void PropertyView::selectionChanged(const QItemSelection& selected,
 
   // Start by clearing the molecule selection
   for (Index i = 0; i < m_molecule->atomCount(); ++i)
-    m_molecule->atom(i).setSelected(false);
+    m_molecule->undoMolecule()->setAtomSelected(i, false);
 
   foreach (const QModelIndex& index, selected.indexes()) {
     if (!index.isValid())
@@ -106,24 +106,24 @@ void PropertyView::selectionChanged(const QItemSelection& selected,
         return;
 
       auto bondPair = m_molecule->bondPair(rowNum);
-      m_molecule->setAtomSelected(bondPair.first, true);
-      m_molecule->setAtomSelected(bondPair.second, true);
+      m_molecule->undoMolecule()->setAtomSelected(bondPair.first, true);
+      m_molecule->undoMolecule()->setAtomSelected(bondPair.second, true);
     } else if (m_type == PropertyType::AngleType) {
 
       if (m_model != nullptr) {
         auto angle = m_model->getAngle(index.row());
-        m_molecule->setAtomSelected(std::get<0>(angle), true);
-        m_molecule->setAtomSelected(std::get<1>(angle), true);
-        m_molecule->setAtomSelected(std::get<2>(angle), true);
+        m_molecule->undoMolecule()->setAtomSelected(std::get<0>(angle), true);
+        m_molecule->undoMolecule()->setAtomSelected(std::get<1>(angle), true);
+        m_molecule->undoMolecule()->setAtomSelected(std::get<2>(angle), true);
       }
     } else if (m_type == PropertyType::TorsionType) {
 
       if (m_model != nullptr) {
         auto torsion = m_model->getTorsion(index.row());
-        m_molecule->setAtomSelected(std::get<0>(torsion), true);
-        m_molecule->setAtomSelected(std::get<1>(torsion), true);
-        m_molecule->setAtomSelected(std::get<2>(torsion), true);
-        m_molecule->setAtomSelected(std::get<3>(torsion), true);
+        m_molecule->undoMolecule()->setAtomSelected(std::get<0>(torsion), true);
+        m_molecule->undoMolecule()->setAtomSelected(std::get<1>(torsion), true);
+        m_molecule->undoMolecule()->setAtomSelected(std::get<2>(torsion), true);
+        m_molecule->undoMolecule()->setAtomSelected(std::get<3>(torsion), true);
       }
     }
   } // end loop through selected
diff --git a/avogadro/qtplugins/select/select.cpp b/avogadro/qtplugins/select/select.cpp
index fa1b7115f6..e65119dcdd 100644
--- a/avogadro/qtplugins/select/select.cpp
+++ b/avogadro/qtplugins/select/select.cpp
@@ -141,7 +141,7 @@ void Select::selectAll()
 {
   if (m_molecule) {
     for (Index i = 0; i < m_molecule->atomCount(); ++i) {
-      m_molecule->atom(i).setSelected(evalSelect(true, i));
+      m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i));
     }
 
     m_molecule->emitChanged(Molecule::Atoms);
@@ -152,7 +152,7 @@ void Select::selectNone()
 {
   if (m_molecule) {
     for (Index i = 0; i < m_molecule->atomCount(); ++i)
-      m_molecule->atom(i).setSelected(false);
+      m_molecule->undoMolecule()->setAtomSelected(i, false);
 
     m_molecule->emitChanged(Molecule::Atoms);
   }
@@ -177,11 +177,13 @@ void Select::selectElement(int element)
   if (!m_molecule)
     return;
 
+  QString undoText = tr("Select Element");
+
   for (Index i = 0; i < m_molecule->atomCount(); ++i) {
     if (m_molecule->atomicNumber(i) == element) {
-      m_molecule->atom(i).setSelected(evalSelect(true, i));
+      m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
     } else
-      m_molecule->atom(i).setSelected(false);
+      m_molecule->undoMolecule()->setAtomSelected(i, false, undoText);
   }
 
   m_molecule->emitChanged(Molecule::Atoms);
@@ -211,29 +213,32 @@ void Select::selectWater()
   if (!m_molecule)
     return;
 
+  QString undoText = tr("Select Water");
+
   for (Index i = 0; i < m_molecule->atomCount(); ++i) {
     auto atomicNumber = m_molecule->atomicNumber(i);
     if (atomicNumber == 8 && isWaterOxygen(i)) {
-      m_molecule->atom(i).setSelected(evalSelect(true, i));
+      m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i));
       continue;
     } else if (atomicNumber == 1) {
       // check if it's attached to a water oxygen
       auto bonds = m_molecule->bonds(i);
       if (bonds.size() != 1 || !isWaterOxygen(bonds[0].getOtherAtom(i).index()))
-        m_molecule->atom(i).setSelected(evalSelect(false, i));
+        m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(false, i), undoText);
       else
-        m_molecule->atom(i).setSelected(evalSelect(true, i));
+        m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
 
       continue;
     }
 
-    m_molecule->atom(i).setSelected(evalSelect(false, i));
+    m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(false, i), undoText);
   }
   // also select water residues (which may be isolated "O" atoms)
   for (const auto residue : m_molecule->residues()) {
     if (residue.residueName() == "HOH") {
       for (auto atom : residue.residueAtoms()) {
-        atom.setSelected(evalSelect(true, atom.index()));
+        Index i = atom.index();
+        m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
       }
     }
   }
@@ -246,11 +251,15 @@ void Select::selectBackboneAtoms()
   // unselect everything
   selectNone();
 
+  QString undoText = tr("Select Backbone");
+
   for (const auto residue : m_molecule->residues()) {
     for (auto atom : residue.residueAtoms()) {
       auto name = residue.getAtomName(atom);
-      if (name == "CA" || name == "C" || name == "N" || name == "O")
-        atom.setSelected(evalSelect(true, atom.index()));
+      if (name == "CA" || name == "C" || name == "N" || name == "O") {
+        Index i = atom.index();
+        m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
+      }
 
       // also select hydrogens connected to the backbone atoms
       if (atom.atomicNumber() == 1) {
@@ -258,8 +267,11 @@ void Select::selectBackboneAtoms()
         if (bonds.size() == 1) {
           auto otherAtom = bonds[0].getOtherAtom(atom.index());
           auto otherName = residue.getAtomName(otherAtom);
-          if (otherName == "CA" || otherName == "C" || otherName == "N" || otherName == "O")
-            atom.setSelected(evalSelect(true, atom.index()));
+          if (otherName == "CA" || otherName == "C" || otherName == "N" ||
+              otherName == "O") {
+            Index i = atom.index();
+            m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
+          }
         }
       }
     }
@@ -273,11 +285,15 @@ void Select::selectSidechainAtoms()
   // unselect everything
   selectNone();
 
+  QString undoText = tr("Select Sidechain");
+
   for (const auto residue : m_molecule->residues()) {
     for (auto atom : residue.residueAtoms()) {
       auto name = residue.getAtomName(atom);
-      if (name != "CA" && name != "C" && name != "N" && name != "O")
-        atom.setSelected(evalSelect(true, atom.index()));
+      if (name != "CA" && name != "C" && name != "N" && name != "O") {
+        Index i = atom.index();
+        m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
+      }
 
       // or is it a hydrogen connected to a backbone atom?
       // (then we don't want to select it)
@@ -287,8 +303,10 @@ void Select::selectSidechainAtoms()
           auto otherAtom = bonds[0].getOtherAtom(atom.index());
           auto otherName = residue.getAtomName(otherAtom);
           if (otherName == "CA" || otherName == "C" || otherName == "N" ||
-              otherName == "O")
-            atom.setSelected(evalSelect(false, atom.index()));
+              otherName == "O") {
+            Index i = atom.index();
+            m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(false, i), undoText);
+          }
         }
       }
     }
@@ -331,13 +349,16 @@ void Select::enlargeSelection()
   maxDistance = sqrt(maxDistance) + 2.5;
   maxDistance *= maxDistance; // square to compare with .squaredNorm() values
 
+  QString undoText = tr("Enlarge Selection");
+
   // now select all atoms within the NEW max distance
   for (Index i = 0; i < m_molecule->atomCount(); ++i) {
     if (!m_molecule->atomSelected(i)) {
       Vector3 displacement = m_molecule->atomPosition3d(i) - center;
       Real distance = displacement.squaredNorm();
-      if (distance < maxDistance)
-        m_molecule->atom(i).setSelected(evalSelect(true, i));
+      if (distance < maxDistance) {
+        m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
+      }
     }
   }
 
@@ -363,14 +384,16 @@ void Select::shrinkSelection()
     maxDistance = 0.0;
   maxDistance *= maxDistance; // square to compare with .squaredNorm() values
 
+  QString undoText = tr("Shrink Selection");
+
   // now select ONLY atoms within the NEW max distance
   for (Index i = 0; i < m_molecule->atomCount(); ++i) {
     Vector3 displacement = m_molecule->atomPosition3d(i) - center;
     Real distance = displacement.squaredNorm();
     if (distance < maxDistance)
-      m_molecule->atom(i).setSelected(evalSelect(true, i));
+      m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
     else
-      m_molecule->atom(i).setSelected(evalSelect(false, i));
+      m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(false, i), undoText);
   }
 
   m_molecule->emitChanged(Molecule::Atoms);
@@ -389,6 +412,8 @@ void Select::selectAtomIndex()
   if (!ok || text.isEmpty())
     return;
 
+  QString undoText = tr("Select Atom");
+
   auto list = text.simplified().split(',');
   foreach (const QString item, list) {
     // check if it's a range
@@ -399,15 +424,14 @@ void Select::selectAtomIndex()
         int start = range.first().toInt(&ok1);
         int last = range.back().toInt(&ok2);
         if (ok1 && ok2) {
-          for (Index i = start; i <= last; ++i) {
-            m_molecule->atom(i).setSelected(evalSelect(true, i));
-          }
+          for (Index i = start; i <= last; ++i)
+            m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
         }
       }
     } else {
       int i = item.toInt(&ok);
       if (ok)
-        m_molecule->atom(i).setSelected(evalSelect(true, i));
+        m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i), undoText);
     }
   }
 
@@ -427,6 +451,8 @@ void Select::selectResidue()
   if (!ok || text.isEmpty())
     return;
 
+  QString undoText = tr("Select Residue");
+
   auto list = text.simplified().split(',');
   foreach (const QString item, list) {
     const QString label = item.simplified(); // get rid of whitespace
@@ -438,7 +464,9 @@ void Select::selectResidue()
       if (index >= 1 && index < residueList.size()) {
         auto residue = residueList[index];
         for (auto& atom : residue.residueAtoms()) {
-          atom.setSelected(evalSelect(true, atom.index()));
+          Index i = atom.index();
+          m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i),
+                                                      undoText);
         }
       } // index makes sense
       continue;
@@ -456,7 +484,9 @@ void Select::selectResidue()
         auto residue = residueList[index];
         if (name == residue.residueName().c_str()) {
           for (auto atom : residue.residueAtoms()) {
-            atom.setSelected(evalSelect(true, atom.index()));
+            Index i = atom.index();
+            m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i),
+                                                        undoText);
           }
         } // check if name matches specified (e.g. HIS57 is really a HIS)
       }   // index makes sense
@@ -466,7 +496,9 @@ void Select::selectResidue()
         if (label == residue.residueName().c_str()) {
           // select the atoms of the residue
           for (auto atom : residue.residueAtoms()) {
-            atom.setSelected(evalSelect(true, atom.index()));
+            Index i = atom.index();
+            m_molecule->undoMolecule()->setAtomSelected(i, evalSelect(true, i),
+                                                        undoText);
           }
         } // residue matches label
       }   // for(residues)
@@ -481,8 +513,8 @@ void Select::invertSelection()
 {
   if (m_molecule) {
     for (Index i = 0; i < m_molecule->atomCount(); ++i)
-      m_molecule->atom(i).setSelected(
-        evalSelect(!m_molecule->atomSelected(i), i));
+      m_molecule->undoMolecule()->setAtomSelected(
+        i, evalSelect(!m_molecule->atomSelected(i), i), tr("Invert Selection"));
     m_molecule->emitChanged(Molecule::Atoms);
   }
 }
diff --git a/avogadro/qtplugins/selectiontool/selectiontool.cpp b/avogadro/qtplugins/selectiontool/selectiontool.cpp
index 41537c1b12..4bd662f001 100644
--- a/avogadro/qtplugins/selectiontool/selectiontool.cpp
+++ b/avogadro/qtplugins/selectiontool/selectiontool.cpp
@@ -287,25 +287,25 @@ void SelectionTool::selectLinkedMolecule(QMouseEvent* e, Index atom)
 void SelectionTool::clearAtoms()
 {
   for (Index i = 0; i < m_molecule->atomCount(); ++i)
-    m_molecule->atom(i).setSelected(false);
+    m_molecule->undoMolecule()->setAtomSelected(i, false);
 }
 
 bool SelectionTool::addAtom(const Index& atom)
 {
-  m_molecule->atom(atom).setSelected(true);
+  m_molecule->undoMolecule()->setAtomSelected(atom, true);
   return true;
 }
 
 bool SelectionTool::removeAtom(const Index& atom)
 {
-  m_molecule->atom(atom).setSelected(false);
+  m_molecule->undoMolecule()->setAtomSelected(atom, false);
   return true;
 }
 
 bool SelectionTool::toggleAtom(const Index& atom)
 {
   Atom a = m_molecule->atom(atom);
-  a.setSelected(!a.selected());
+  m_molecule->undoMolecule()->setAtomSelected(atom, !a.selected());
   return a.selected();
 }