diff --git a/modules/gui/doc/gui.rst b/modules/gui/doc/gui.rst
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@@ -0,0 +1,111 @@
+:mod:`~ost.gui` -- Graphical User Interface
+================================================================================
+
+.. module:: ost.gui
+
+The GUI of OpenStructure is designed to be intuitive, flexible and extensible.
+Most of the widgets are organized in a big main window which is divided into
+four parts: the main area and three panels containing one or more
+smaller widgets:
+
+.. image:: images/100208_OpenStructure_UI_Colored.png
+
+The panels primarily contains widgets interacting with the 3D window.
+All parts of the GUI are exported to Python and can be expanded with
+C++ Qt widgets as well as with PyQt widgets. Learn more about :doc:`python_cpp`.
+
+.. toctree::
+
+ python_cpp
+ scene_win
+ inspector_gadget
+ tools
+ drag_and_drop
+ python_shell
+ menubar
+ panels
+ sequence_viewer
+
+Tools
+--------------------------------------------------------------------------------
+OpenStructure has several :class:`Tool` which are all listed in the toolbar
+close to the 3D window. A tool is activated upon selecting it in the toolbar.
+Input events are sent to the tool as long as the `Ctrl` key (`Cmd` on Mac) is
+pressed. For example the rigid body manipulator will rotate and shift the
+currently selected nodes in the scene win. Upon releasing `Ctrl`, the events are
+sent to the camera, making it possible to rapidly switch between adjusting the
+viewing angle of the camera and manipulating the position and orientation of
+scene objects.
+
+.. image:: images/100208_Tools.png
+
+The example `Write a Tool in Python` demonstrates how to add a simple tool
+(written in python) to OpenStructure.
+
+Drag and Drop support
+--------------------------------------------------------------------------------
+The user interface of OpenStructure supports drag and drop events. Every file
+format that is supported by Openstructure can be opened by dragging and dropping
+it on the main window. When a python script (ending with .py) is being dropped
+on the UI, the script will be executed. For any other file type (for example PDB
+files, images and density maps), OpenStructure will try to load the file and
+display it in the 3D window, in the data viewer for images or in the sequence
+viewer.
+
+Python Shell
+--------------------------------------------------------------------------------
+OpenStructure has a integrated python shell which allows you interactively enter
+Python commands. Learn more about it in :doc:`python_shell`-Tutorial.
+
+The Side Panels
+--------------------------------------------------------------------------------
+View Modes
+^^^^^^^^^^
+Each :class:`PanelBar` can have different :class:`PanelWidgetContainer` also
+called view modes. View modes can display the widgets which are held by the Side
+Panel in a different style. Every panel has the splitter and the tabbed view
+mode.
+The view mode can be changed in the Window menu of the Menubar.
+
+Drag and Drop
+^^^^^^^^^^^^^
+The widgets which are held by a Side Panel can be moved to an other position in
+the panel or even to another side panel. The widget can be moved by simply
+clicking on the border of the widget and drag and drop it to the desired
+position. The drag and drop feature is currently only supported by the splitter
+view mode.
+
+Adding a custom Widget
+^^^^^^^^^^^^^^^^^^^^^^
+The Left-, Bottom- and Right-Panel are organized by the :class:`Panels`-class.
+It is only possible to display a widget which is in the :class:`WidgetPool` of
+the panels class. Once a widget is in the pool all the methods of the Panels
+class can be used to display / hide the widget in any position of the panels.
+The Example `Add a custom Widget` describes, how to add a fancy PyQt Widget to
+the widget pool and finally display it in the right side bar.
+OpenStructure remembers the size and location of a Widget. So, OpenStructure
+should look the same after restarting it.
+
+Main Area
+--------------------------------------------------------------------------------
+Adding an own Widget
+^^^^^^^^^^^^^^^^^^^^
+The :class:`MainArea` is a mdi (multi document interface). Therefore it's
+possible to display multiple widgets in it. The example `Add a Widget to MDI`
+demonstrates how to add a widget to the MDI area.
+
+Menubar
+--------------------------------------------------------------------------------
+Adding an new Menupoint
+^^^^^^^^^^^^^^^^^^^^^^^
+It is really straightforward to add a custom menupoint. Since the menubar is
+exported to Python it is even easier to create such e menupoint. See the example
+`Adding a Menu` which describes how this is done within python and PyQt.
+
+Nice to know
+---------------------------------------------------------------------------------
+As you might have noticed nearly every gui example needs the :class:`GostyApp`
+and the :class:`Perspective` within the code. Gosty app is a singleton class
+which has getter methods to all important gui classes. The perspective class has
+all the information about the layout of the whole application, it is accessible
+over the gosty app instance.
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diff --git a/modules/gui/doc/inspector_gadget.rst b/modules/gui/doc/inspector_gadget.rst
new file mode 100644
index 0000000000000000000000000000000000000000..116746d1ef090a10f1c110a08434476ed8b81392
--- /dev/null
+++ b/modules/gui/doc/inspector_gadget.rst
@@ -0,0 +1,11 @@
+The Inspector Gadget
+================================================================================
+.. currentmodule:: ost.gui
+
+With our Inspector Gadget it is straightforward to modify rendering and coloring
+options of scene objects without using the keyboard:
+
+.. image:: images/100614_Inspector_gadget.png
+
+The render and coloring options affect only the currently selected objects of
+the scene win. The Shortcut `Ctrl+I` toggles the visibility of the inspector.
diff --git a/modules/gui/doc/python_cpp.rst b/modules/gui/doc/python_cpp.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9b30010fee0b2257936c4ae8b885cc5e38c249ae
--- /dev/null
+++ b/modules/gui/doc/python_cpp.rst
@@ -0,0 +1,25 @@
+Mixing PyQt and C++ Widgets
+================================================================================
+.. currentmodule:: ost.gui
+
+PyQt4 is a set of python bindings for Qt4. The exposure from C++ to Python is
+done with SIP, which has a different mechanism than boost::python.
+
+To access a exported boost::python Qt-Object from python we provide a method
+which wraps the Object into a Python SIP Object.
+
+ .. code-block:: python
+
+ seq_viewer = gui.SequenceViewer() # Create SequenceViewer Object
+ qobj = seq_viewer.qobject #Get Python SIP Object
+ print qobj.size() # Call function on QWidget
+
+The other way around, each boost::python Qt Object accepts python objects as
+input for Qt Objects. It handles the cast to a C++ Qt Object internally.
+
+ .. code-block:: python
+
+ persp=gui.GostyApp.Instance().perspective
+ test=persp.GetMenu("Test") #Get boost::python qobject
+ test_action = QtGui.QAction('&Test me', test) #Create Python SIP Object
+ test.addAction(test_action) #Add Action to boost::python object
diff --git a/modules/gui/doc/python_shell.rst b/modules/gui/doc/python_shell.rst
new file mode 100644
index 0000000000000000000000000000000000000000..780bd42bfba20e774da06af7e8356ffb0fc46edd
--- /dev/null
+++ b/modules/gui/doc/python_shell.rst
@@ -0,0 +1,40 @@
+The Python Shell
+================================================================================
+.. currentmodule:: ost.gui
+
+.. class:: PythonShell
+
+OpenStructure has a powerful Python Shell which has some handy features. It is
+completely integrated into OpenStructure and allows you enter Python code.
+
+Multi line detection
+--------------------------------------------------------------------------------
+The Python Shell detects automatically if a code block is complete or not.
+For example a simple print statement in the command line is a complete code
+block. Therefore the code will be executed after pressing enter:
+
+.. image:: images/100210_single_line.png
+
+When a multiline codeblock (like a for loop or an if instruction) is being
+entered in the command line, the code is not executed until the code block is
+complete:
+
+.. image:: images/100210_multi_line.png
+
+When a code block is not complete, pressing enter appends an empty line at the
+end of the code block. To execute such a code block, you simply have to press
+enter twice.
+
+Auto completion
+--------------------------------------------------------------------------------
+After pressing tab in the Python Shell, it returns you possible extensions
+to your entered text. This feature can be used for completing variable names
+or functions:
+
+.. image:: images/100210_auto_completion.png
+
+It is also possible to complete a file system path string. By pressing tab while
+editing a string, the shell displays all file or folders of the given
+directory:
+
+.. image:: images/100210_path_completion.png
diff --git a/modules/gui/doc/scene_win.rst b/modules/gui/doc/scene_win.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8cbd6875219bca8d774bb359863e667d6a5c6b1f
--- /dev/null
+++ b/modules/gui/doc/scene_win.rst
@@ -0,0 +1,124 @@
+Scene Window
+================================================================================
+.. currentmodule:: ost.gui
+
+The scene win holds a list of all graphical objects currently registered to
+the :class:`gfx.Scene`.
+
+.. image:: images/100208_Scene_Win.png
+
+Every node of the graphical scene tree is shown as a subnode of the scene. It
+is possible to select one or more objects in the scenewin (`ctrl + <left mouse>`
+). The available actions of the context menu are applied to all currently
+selected objects.
+
+.. class:: SceneWin
+
+ .. method:: GetContextMenu()
+
+ Returns the :class:`ContextMenu`-instance.
+
+ :rtype: ContextMenu
+
+ .. method:: GetQObject()
+
+ Get the SIP-QObject (QWidget), learn more about :doc:`python_cpp`.
+
+ :rtype: PyQt4.QWidget
+
+ .. method:: Hide()
+
+ Hide the Widget
+
+ .. method:: Show()
+
+ Shows the Widget
+
+Context Menu
+--------------------------------------------------------------------------------
+
+The Context Menu of the Scene Window is context sensitive. So, dependent on what
+is selected in the :class:`SceneWin` the context menu changes.
+
+Context menu of an entity
+ .. image:: images/100614_entity_context_menu.png
+
+Context menu of an entity view
+ .. image:: images/100614_context_menu_view.png
+
+It is possible to extend the Context Menu from python, by creating a QAction and
+add it to the ContextMenu-Class. If you want to display the action only for
+certain objects / states, you can pass flags which marks when the action should
+be shown.
+
+ .. code-block:: python
+
+ cm=gui.GostyApp.Instance().scene_win.GetContextMenu()
+ action = QtGui.QAction("Test single entity", cm.qobject)
+ cm.AddAction(action, gui.ContextActionType.ENTITY | gui.ContextActionType.SINGLE)
+
+.. class:: ContextMenu
+
+ The ContextMenu is shown whenever the user presses `<right click>` on the :class:`SceneWin`
+
+ .. method:: AddAction(action, flags)
+
+ Adds the given action to the context menu of the scene window.
+
+ :param action: The Action which should be displayed in the context menu
+
+ :type action: :class:`QtCore.QAction`
+
+ :param flags: Flags that indicates, when the context_menu should be active. The action
+ will be shown, when all flags are true.
+
+ :type flags: :data:`ContextActionTypes`
+
+
+ .. method:: GetQObject()
+
+ Get the SIP-QObject (QObject), learn more about :doc:`python_cpp`.
+
+ :rtype: PyQt4.QObject
+
+
+.. data:: ContextActionType
+
+ It is possible to specify flags for new :class:`ContextMenu` actions of the :class:`SceneWin`
+ These flags are used, to specify when the action should be shown on the scene window. The
+ actions can be combined by `oring` them (|). When flags are combined with an `or`, the
+ resulting object is a :data:`ContextActionTypes`-object.
+ The following flags are defined by default:
+
+ * NOT_SCENE
+ All selected objects are not the root node
+ * GFX_OBJECT
+ All selected objects are :class:`gfx.GfxObj`
+ * ENTITY
+ All selected objects are :class:`gfx.Entity`
+ * MAP
+ All selected objects are :class:`gfx.MapIso`
+ * ENTITY_VIEW
+ All selected objects are parts of the same Entity (either Queries or Views)
+ * CUSTOM_VIEW
+ All selected objects are named views (created by the user)
+ * NOT_HIDDEN
+ All selected objects are visible (can not be combined with the ENTITY_VIEW flag)
+ * NOT_VISIBLE
+ All selected objects are hidden (can not be combined with the ENTITY_VIEW flag)
+ * SINGLE
+ There is only one selected object in the :class:`SceneWin`
+ * MULTI
+ There are multiple objects selected object in the :class:`SceneWin`
+
+.. data:: ContextActionTypes
+
+ When multiple :data:`ContextActionType` objects are being combined with an or (|) you will get an
+ :data:`ContextActionTypes`-Object.
+
+ .. code-block:: python
+
+ ctx_act_types = gui.ContextActionType.ENTITY | gui.ContextActionType.SINGLE
+
+
+
\ No newline at end of file
diff --git a/modules/gui/doc/sequence_viewer.rst b/modules/gui/doc/sequence_viewer.rst
new file mode 100644
index 0000000000000000000000000000000000000000..87c2ae384729475de71273cc0f78d1081457d298
--- /dev/null
+++ b/modules/gui/doc/sequence_viewer.rst
@@ -0,0 +1,178 @@
+The Sequence Viewer
+================================================================================
+.. currentmodule:: ost.gui
+
+The sequence viewer of OpenStructure can be used to display sequences or
+alignments.
+
+The following example adds an alignment to a sequence viewer and shows it in a
+new sequence viewer instance:
+
+.. code-block:: python
+
+ aln=io.LoadAlignment('sh2.aln')
+ v=gui.SequenceViewer()
+ v.AddAlignment(aln)
+ v.Show()
+
+Core Features
+--------------------------------------------------------------------------------
+
+Display styles
+^^^^^^^^^^^^^^
+It is possible to display the data in different ways. To change the display
+style, click the tool icon of the menubar and select the
+display style from the list.
+
+ .. image:: images/100615_select_display_style.png
+
+For the moment there are four different display styles:
+
+
+
+ **1. Highlight propteries**
+
+ .. image:: images/100615_property_type.png
+ :width: 500pt
+
+ Color groups of amino acids
+
+ ===== ====== ====== ===== === ==== ====
+ grey orange yellow green red blue cyan
+ ===== ====== ====== ===== === ==== ====
+ G F C S K D P
+ A Y M T R E
+ V W H N
+ L Q
+ I
+ ===== ====== ====== ===== === ==== ====
+
+
+ **2. Secondary structure**
+
+ .. image:: images/100615_secondary_structure.png
+ :width: 500pt
+
+ Display secondary structure information
+
+ This mode is only available, when a :class:`mol.EntityView` is connected to
+ the sequence.
+
+ **3. Highlight conservation 1**
+
+ .. image:: images/100615_conservation_1.png
+ :width: 500pt
+
+ Display conservation
+
+ This display style uses the :meth:`seq.alg.Conservation`-Algorithm which calculates
+ the Conservation for each column. This Mode is only available for alignments.
+
+ **4. Highlight conservation 2**
+
+ .. image:: images/100615_conservation_2.png
+ :width: 500pt
+
+ Display conservation
+
+ This implementation of conservation colors the columns grey, if all amino acids are
+ from the same type. If all amino acids are from the same group, it colors the column with
+ a light grey. Otherwise the column is colored white. This Mode is also only available for
+ alignments.
+
+
+Zoom
+^^^^
+
+With the sequence viewer of Openstructure it is possible to zoom in and out `<ctrl + mousewheel>`.
+
+ .. image:: images/100616_zoom_in.png
+
+ Zoom in, if you lost your glasses at home
+
+ .. image:: images/100616_zoom_out.png
+
+ Zoom out, if you need a better overview of the sequence
+
+Copy and Paste
+^^^^^^^^^^^^^^
+
+It is possible to copy sequence text from the sequence viewer by pressing `<ctrl + c>`. If you paste
+the text (for example into a text editor), all the gaps will be filled with `-`.
+
+ .. image:: images/100616_copy_paste.png
+
+Search
+^^^^^^
+
+With `<ctrl + f>` you can show or hide the search bar which help you finding parts of a sequence.
+
+ .. image:: images/100617_search_bar.png
+
+.. class:: SequenceViewer
+
+The SequenceViewer class represents a graphical sequence viewer. To see the sequences of a :class:`gfx.Entity`, you
+can use the :meth:`AddEntity` method. If you want to load an alignment, the :meth:`AddAlignment` method can be used.
+
+ .. method:: AddAlignment(alignment)
+
+ Add :class:`seq.AlignmentHandle` to SequenceViewer.
+
+ :param alignment: an alignment instance
+ :type alignment: :class:`seq.AlignmentHandle`
+
+ .. method:: RemoveAlignment(alignment)
+
+ Remove alignment from sequenceviewer.
+
+ :param alignment: an alignment instance
+ :type alignment: :class:`seq.AlignmentHandle`
+ :rtype: None
+
+ .. method:: ChangeDisplayMode(style [, obj : None])
+
+ Change the display style of all alignments and sequences to the given style. If the obj parameter is given, it
+ changes only the display style of the given object.
+
+ If the style is not known, nothing happens
+
+ See also :meth:`GetDisplayModes`, :meth:`GetCurrentDisplayMode`
+
+ :param style: The display style
+ :type style: :class:`string`
+ :param obj: The object you would like to change
+ :type obj: :class:`gfx.Entity`, :class:`seq.AlignmentHandle`
+
+
+ .. method:: GetCurrentDisplayMode([obj : None])
+
+ Returns the current display style. If there are objects with different display styles, " " will be returned
+ otherwise the string of the display style.
+
+ :rtype: str
+ :param obj: The object you would like to get the display style
+ :type obj: :class:`gfx.Entity`, :class:`seq.AlignmentHandle`
+
+ .. method:: GetDisplayModes([obj : None])
+
+ Returns a list with all available display styles. If you pass an object, you will get only the display styles for
+ the given object.
+
+ :rtype: StringList
+ :param obj: The object you would like to get all display styles
+ :type obj: :class:`gfx.Entity`, :class:`seq.AlignmentHandle`
+
+ .. method:: GetQObject()
+
+ Get the SIP-QObject (QWidget), learn more about :doc:`python_cpp`.
+
+ :rtype: PyQt4.QWidget
+
+ .. method:: Hide()
+
+ Hide the Widget
+
+ .. method:: Show()
+
+ Shows the Widget
+
diff --git a/modules/index.rst b/modules/index.rst
index cdb3284d5b4d8ba64311e151052d0200d4a1d66f..c70e751c08e24eda54a2318c11ac46f829b97810 100644
--- a/modules/index.rst
+++ b/modules/index.rst
@@ -28,6 +28,7 @@ Modules
seq/base/seq
base/base
io/io
+ gui/gui
Extending OpenStructure
--------------------------------------------------------------------------------