diff --git a/doc/source/intro-01.rst b/doc/source/intro-01.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6c77564e455b7f79f300d770b1576ac1be6df926
--- /dev/null
+++ b/doc/source/intro-01.rst
@@ -0,0 +1,229 @@
+Introduction to the :mod:`~ost.mol` Module
+================================================================================
+
+For the course of this tutorial, we assume that you have :ref:`DNG up and running <start-dng>`.
+
+Loading and inspecting a protein structure
+--------------------------------------------------------------------------------
+
+The code to load and save structures is not directly part of the mol module, but rather lives in a module dedicated to input and output of any kind of data: The
+:mod:`~ost.io` module. We will be using functions of this module to load
+structures.
+
+One of the most commonly used file formats for macromolecular structures are
+PDB (Brookhaven Protein Data Bank) files. The official name for molecules
+stored in a PDB file is an *entity* and we decided to follow this convention
+in OpenStructure. You will hear this word all the time, but you can replace
+the word entity with molecule (or most of the time even protein) in your head.
+
+Loading a PDB file leaves you with an :class:`~ost.mol.EntityHandle`. This is
+the central class holding together :class:`chains <ost.mol.ChainHandle>`,
+:class:`residues <ost.mol.ResidueHandle>` and
+:class:`atoms <ost.mol.AtomHandle>` in a straight-forward hierarchy. This
+hierarchy will always be intact: there are no atoms without a residue they
+belong to and no residues without chains which have to belong to an entity.
+Beside the molecule itself, there are a lot of additional attributes stored in
+the entity, like the
+:attr:`centre of mass <ost.mol.EntityHandle.center_of_mass>`.
+
+To load a PDB file, simply type
+
+.. code-block:: python
+
+ fragment=io.LoadPDB('/path/to/examples/code_fragments/entity/fragment.pdb')
+
+This will load the fragment from the specified file 'fragment.pdb' and store the
+result in fragment. The :func:`~ost.io.LoadPDB` has many options, which, for
+simplicity will not be discussed here. If you want to know more about the
+function, type:
+
+.. code-block:: python
+
+ help(io.LoadPDB)
+
+or read the :func:`online documentation <ost.io.LoadPDB>`.
+
+The loaded structure is an instance of :class:`~ost.mol.EntityHandle` which offers a comprehensive interface to inspect an manipulate molecular structures. Now let's inspect what we just loaded:
+
+.. code-block:: python
+
+ print len(fragment.chains), fragment.chains
+ print len(fragment.residues), fragment.residues
+ print len(fragment.atoms), fragment.atoms
+
+As you can see, our fragment consists of one peptide chain of 12 amino acids and
+has 81 atoms in total. Now let's examine our fragment in more detail. Enter the
+command
+
+.. code-block:: python
+
+ for residue in fragment.residues:
+ print residue, 'has', len(residue.atoms), 'atom(s).'
+ for atom in residue.atoms:
+ print ' ', atom.name, atom.pos
+
+
+This will group the atoms by residue. And, for completeness, we will first group them by chain, then by residues.
+
+.. code-block:: python
+
+ for chain in fragment.chains:
+ print 'chain', chain.name, 'has', len(chain.residues), 'residue(s)'
+ for residue in chain.residues:
+ print ' ', residue, 'has', len(residue.atoms), 'atom(s).'
+ for atom in residue.atoms:
+ print ' ', atom.name, atom.pos
+
+A protein fragment would not be complete without bonds: Let's see
+what bonds we have in there:
+
+.. code-block:: python
+
+ for bond in fragment.bonds:
+ print bond
+
+Let There Be Shiny Graphics
+--------------------------------------------------------------------------------
+
+For visually inspecting the fragment, we now create a graphical representation
+of the entity. The graphical representation is completely separate from the :class:`~ost.mol.EntityHandle` class. This is on purpose. When writing processing scripts, usually no graphical representation is required and things would be slowed down without any reason. The following code will take our fragment and initialise a :class:`gfx.Entity<ost.gfx.Entity>`, add it to the scene, and center the camera on it.
+
+.. code-block:: python
+
+ go=gfx.Entity("Fragment", fragment)
+ scene.Add(go)
+ scene.CenterOn(go)
+
+
+Now you will see the fragment in the 3D window.
+
+Use the mouse to rotate, zoom in and shift the camera. Double clicking on an
+atom will center the camera on that atom. If you want to learn more about the
+:mod:`~ost.gfx` module, you are encouraged to read :doc:`the gfx
+intro<intro-03>` and the :mod:`gfx documentation<ost.gfx`.
+
+Introduction to Views
+--------------------------------------------------------------------------------
+
+Often during processing and visualisation of data, only parts of a protein
+structure are of interest. This realisation has had a major impact on the design
+of OpenStructure and is tied very deeply into the core of the framework.
+Subparts of structure are modelled as so-called :class:`EntityViews
+<ost.mol.EntityView>`. You can think of them as a selection of chains, residues,
+atoms and bonds of an entity. A views has almost the same interface as the
+underlying entity, making it very easy to mix entity views with handles in
+Python due to the dynamic nature of the language. An algorithm that is written
+for entities will almost always (with some care) also work for
+:class:`EntityHandles <ost.mol.EntityHandle>`. This is referred to as
+`duck-typing <http://en.wikipedia.org/wiki/Duck_typing>`_ (I don' t care if it
+is a duck as long as it looks like a duck), a concept used all over the place in Python.
+
+The view consists of one chain, one residue and two atoms. Again the same rule
+applies: No atom can be part of the view without it's residue. In this example,
+no bonds are included, since there is at most one atom per bond in the original structure.
+
+To familiarize yourself with the concept of views, we will use the fragment in
+the 3D window.
+
+We will use several ways to select parts of our fragment:
+ * By using a dedicated query language
+ * By manually constructing a view
+
+The Query Language
+--------------------------------------------------------------------------------
+
+The first way to select parts of a structure is with a dedicated mini-language,
+called :doc:`the query language <mol/base/query>`. In the Python Shell, type
+
+.. code-block:: python
+
+ go.selection=fragment.Select('')
+
+The code performs a selection on the fragment and assigns the resulting view to
+the selection of the graphical object. A green halo will be displayed around the
+selected parts (image in the middle).
+
+.. image:: sel.png
+
+As you can see the previous statement created a “full view”, containing all the
+chains, residues, atoms and bonds. To select lysine residues, type
+
+.. code-block:: python
+
+ go.selection=fragment.Select('rname=LYS')
+
+
+As you can see (image on the right), the only lysine residue is now
+highlighted in the 3D window, because it was the only one matching the predicate
+"residue name must be equal to LYS". Several such predicates can be combined
+with boolean operators such as *and* and *or*. To select residues with residue
+number 1 to 3, the following statement will do the job:
+
+.. code-block:: python
+
+ go.selection=fragment.Select('rnum>=1 and rnum<=3')
+
+but this is very cumbersome. That's why there is a shortcut to this statement.
+You can specify a range of values.
+
+.. code-block:: python
+
+ go.selection=fragment.Select('rnum=1:3')
+
+For a complete description of what you can do with the query language, have a
+look at the :doc:`../mol/base/query`.
+
+
+Constructing Views Manually
+--------------------------------------------------------------------------------
+
+Sometimes the query language Is Not Enough (TM). For these cases the
+construction of manual entities becomes neccessary. This is pretty straight
+forward:
+
+.. code-block:: python
+
+ view=fragment.CreateEmptyView()
+ ca=fragment.FindAtom('A', mol.ResNum(1), 'CA')
+ cb=fragment.FindAtom('A', mol.ResNum(1), 'CB')
+ view.AddAtom(ca)
+ view.AddAtom(cb)
+ go.SetSelection(view)
+
+The last step sets our constructed view as the current selection, displaying it
+in the 3D window. As you can see, C-alpha and C-beta of the first residue are
+not connected by bonds, even though both atoms are in the view. You have either
+to add the bond manually with
+
+.. code-block:: python
+
+ ca_cb=ca.FindBondToAtom(cb)
+ view.AddBond(ca_cb)
+
+Or, as a very convenient shortcut
+:meth:`view.AddAllInclusiveBonds()<ost.mol.EntityView.AddAllInclusiveBonds>` to
+add all bonds that have both bonding partners in the view.
+
+Don't forget to update the selection of the graphics object to see what view you
+have created.
+
+Saving an Entity
+--------------------------------------------------------------------------------
+
+Saving an entity (or a view) is a breeze:
+
+.. code-block:: python
+
+ io.SavePDB(fragment, 'full.pdb')
+
+will save the full fragment. To save only the backbone atoms, we can first
+select the backbone atoms and then save it:
+
+.. code-block:: python
+
+ io.SavePDB(fragment.Select('aname=CA,C,N,O'), 'backbone.pdb')
+
+That's it for the mol module. Continue with :doc:`part two<intro-02>` of the
+tutorial.
+
+.. LocalWords: attr
diff --git a/doc/source/intro.rst b/doc/source/intro.rst
new file mode 100644
index 0000000000000000000000000000000000000000..86bf6dc1e1df0e095461b8041e0e75da910e9676
--- /dev/null
+++ b/doc/source/intro.rst
@@ -0,0 +1,69 @@
+A gentle introduction to OpenStructure
+================================================================================
+
+In this tutorial you will be learning by example how to use the OpenStructure
+framework.
+
+We assume that you already have a version of OpenStructure installed. If not,
+please refer to :doc:`install`.
+
+
+What will be covered in this tutorial?
+--------------------------------------------------------------------------------
+
+This tutorial is aimed at users that would like to get their hands dirty and
+execute commands in Python and write scripts rather clicking their way through a
+shiny user interface. The user interface of OpenStructure is in a very early
+state anyway that you probably won't go far by clicking your way through...
+
+The tutorial is divided into several parts. The first part of the tutorial is a
+walk-through of the basic functionality you will be using in your everyday work, followed by an introduction to the :mod:`~ost.mol`, :mod:`~ost.img` and :mod:`~ost.seq` modules.
+
+.. toctree::
+ :maxdepth: 1
+
+ intro-01
+ intro-02
+ intro-03
+
+.. _start-dng:
+
+Getting ready to rumble
+--------------------------------------------------------------------------------
+
+The files we will be using in the tutorial are available in the examples
+directory that comes with OpenStructure. Depending on your platform, the
+examples are located at a different location:
+
+ * on *MacOS X* the files are located inside the application bundle (DNG.app).
+ The file browser will automatically point to the examples.
+ * on *Linux* PREFIX/share/openstructure/examples, where PREFIX is
+ the path to the directory containing OpenStructure.
+
+Starting DNG
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The graphical user interface of OpenStructure is called DNG (Dino/DeepView Next
+Generation). To start it,
+
+ * on *MacOS X* double click DNG.app
+ * on *Linux* fire up a terminal change into the OpenStructure installation
+ directory and type 'bin/dng'. If you have the binary directory in the PATH,
+ typing dng is sufficient.
+
+Interactive Python Shell
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Now we will enter commands in the Python Shell (in the screenshot above, the
+python shell is located at the bottom of the main window). If you want to get
+more information on any object, function or class, the python help command may
+be useful. For example:
+
+ .. code-block:: python
+
+ # get list of methods of EntityView
+ help(mol.EntityView)
+ # get help for method Select
+ help(mol.EntityView.Select)
+
+Continue with :doc:`part one <intro-01>`