diff --git a/avogadro/qtplugins/manipulator/manipulatewidget.ui b/avogadro/qtplugins/manipulator/manipulatewidget.ui
index 9cee9494bc..5ec82d36ad 100644
--- a/avogadro/qtplugins/manipulator/manipulatewidget.ui
+++ b/avogadro/qtplugins/manipulator/manipulatewidget.ui
@@ -6,8 +6,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>337</width>
-    <height>247</height>
+    <width>371</width>
+    <height>292</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -103,6 +103,39 @@
      </item>
     </layout>
    </item>
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout_3">
+     <property name="topMargin">
+      <number>0</number>
+     </property>
+     <item>
+      <widget class="QLabel" name="label_2">
+       <property name="text">
+        <string>Rotate around:</string>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QComboBox" name="rotateComboBox">
+       <item>
+        <property name="text">
+         <string>Origin</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>Center of Molecule</string>
+        </property>
+       </item>
+       <item>
+        <property name="text">
+         <string>Center of Selection</string>
+        </property>
+       </item>
+      </widget>
+     </item>
+    </layout>
+   </item>
    <item>
     <layout class="QGridLayout" name="gridLayout_2">
      <item row="2" column="0">
@@ -174,23 +207,30 @@
        </property>
       </widget>
      </item>
-     <item row="0" column="0">
-      <widget class="QLabel" name="label_2">
+    </layout>
+   </item>
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout_4">
+     <property name="topMargin">
+      <number>0</number>
+     </property>
+     <item>
+      <widget class="QLabel" name="label_9">
        <property name="text">
-        <string>Rotate around:</string>
+        <string>Move:</string>
        </property>
       </widget>
      </item>
-     <item row="0" column="1">
-      <widget class="QComboBox" name="rotateComboBox">
+     <item>
+      <widget class="QComboBox" name="moveComboBox">
        <item>
         <property name="text">
-         <string>Origin</string>
+         <string>Selected Atoms</string>
         </property>
        </item>
        <item>
         <property name="text">
-         <string>Geometry</string>
+         <string>Everything Else</string>
         </property>
        </item>
       </widget>
diff --git a/avogadro/qtplugins/manipulator/manipulator.cpp b/avogadro/qtplugins/manipulator/manipulator.cpp
index fbe0fbc66c..69af565abe 100644
--- a/avogadro/qtplugins/manipulator/manipulator.cpp
+++ b/avogadro/qtplugins/manipulator/manipulator.cpp
@@ -50,7 +50,7 @@ Manipulator::Manipulator(QObject* parent_)
   m_activateAction->setToolTip(
     tr("Manipulation Tool\n\n"
        "Left Mouse: \tClick and drag to move atoms\n"
-       "Right Mouse: \tClick and drag to rotate selected atoms.\n"));
+       "Right Mouse: \tClick and drag to rotate atoms.\n"));
   setIcon();
   connect(m_toolWidget->buttonBox, SIGNAL(clicked(QAbstractButton*)), this,
           SLOT(buttonClicked(QAbstractButton*)));
@@ -99,20 +99,27 @@ void Manipulator::buttonClicked(QAbstractButton* button)
     return;
   }
 
+  bool moveSelected = (m_toolWidget->moveComboBox->currentIndex() == 0);
+
   // apply values
   Vector3 delta(m_toolWidget->xTranslateSpinBox->value(),
                 m_toolWidget->yTranslateSpinBox->value(),
                 m_toolWidget->zTranslateSpinBox->value());
 
-  translate(delta);
+  translate(delta, moveSelected);
 
   Vector3 rotation(m_toolWidget->xRotateSpinBox->value(),
                    m_toolWidget->yRotateSpinBox->value(),
                    m_toolWidget->zRotateSpinBox->value());
   Vector3 center(0.0, 0.0, 0.0);
 
-  // Check if we're rotating around the origin or the centroid
+  // Check if we're rotating around the origin, the molecule centroid
+  // or the center of selected atoms
+  // == 0 is the default = origin
   if (m_toolWidget->rotateComboBox->currentIndex() == 1) {
+    // molecule centroid
+    center = m_molecule->molecule().centerOfGeometry();
+  } else if (m_toolWidget->rotateComboBox->currentIndex() == 2) {
     // center of selected atoms
     unsigned long selectedAtomCount = 0;
     for (Index i = 0; i < m_molecule->atomCount(); ++i) {
@@ -124,16 +131,13 @@ void Manipulator::buttonClicked(QAbstractButton* button)
     }
     if (selectedAtomCount > 0)
       center /= selectedAtomCount;
-
-  } else {
-    center = m_molecule->molecule().centerOfGeometry();
   }
 
   // Settings are in degrees
 #ifndef DEG_TO_RAD
 #define DEG_TO_RAD 0.0174532925
 #endif
-  rotate(rotation * DEG_TO_RAD, center);
+  rotate(rotation * DEG_TO_RAD, center, moveSelected);
 
   m_molecule->emitChanged(Molecule::Atoms | Molecule::Modified);
 }
@@ -280,10 +284,12 @@ QUndoCommand* Manipulator::mouseMoveEvent(QMouseEvent* e)
   return nullptr;
 }
 
-void Manipulator::translate(Vector3 delta)
+void Manipulator::translate(Vector3 delta, bool moveSelected)
 {
   for (Index i = 0; i < m_molecule->atomCount(); ++i) {
-    if (!m_molecule->atomSelected(i))
+    if (moveSelected && !m_molecule->atomSelected(i))
+      continue;
+    else if (!moveSelected && m_molecule->atomSelected(i))
       continue;
 
     Vector3 currentPos = m_molecule->atomPosition3d(i);
@@ -291,7 +297,7 @@ void Manipulator::translate(Vector3 delta)
   }
 }
 
-void Manipulator::rotate(Vector3 delta, Vector3 centroid)
+void Manipulator::rotate(Vector3 delta, Vector3 centroid, bool moveSelected)
 {
   // Rotate the selected atoms about the center
   // rotate only selected primitives
@@ -311,7 +317,9 @@ void Manipulator::rotate(Vector3 delta, Vector3 centroid)
   fragmentRotation.translate(-centroid);
 
   for (Index i = 0; i < m_molecule->atomCount(); ++i) {
-    if (!m_molecule->atomSelected(i))
+    if (moveSelected && !m_molecule->atomSelected(i))
+      continue;
+    else if (!moveSelected && m_molecule->atomSelected(i))
       continue;
 
     Vector3 currentPos = m_molecule->atomPosition3d(i);
diff --git a/avogadro/qtplugins/manipulator/manipulator.h b/avogadro/qtplugins/manipulator/manipulator.h
index ed0a53941f..642744ecec 100644
--- a/avogadro/qtplugins/manipulator/manipulator.h
+++ b/avogadro/qtplugins/manipulator/manipulator.h
@@ -70,8 +70,8 @@ public slots:
   void updatePressedButtons(QMouseEvent*, bool release);
 
   void resetObject() { m_object = Rendering::Identifier(); }
-  void translate(Vector3 delta);
-  void rotate(Vector3 delta, Vector3 centroid);
+  void translate(Vector3 delta, bool moveSelected = true);
+  void rotate(Vector3 delta, Vector3 centroid, bool moveSelected = true);
   void tilt(Vector3 delta, Vector3 centroid);
 
   QAction* m_activateAction;