correct some typos

modules/doc/contributing.rst

@@ -14,7 +14,7 @@ Even though, technically, there is no such a thing as a central repository in gi
 
 .. code-block:: bash
 
-  git clone https:/dng.biozentrum.unibas.ch/git/ost.git
+  git clone https://dng.biozentrum.unibas.ch/git/ost.git
 
 
 For information on how to install OpenStructure from source, refer to :doc:`install`. 

modules/doc/intro-01.rst

 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>`.
+For the course of this tutorial, we assume that you have :ref:`DNG up and running <start-dng>`.
 
 Loading and inspecting a protein structure
 --------------------------------------------------------------------------------
@@ -21,7 +21,7 @@ To load a PDB file, simply type
 
 .. code-block:: python
 
-   fragment=io.LoadPDB('/path/to/examples/entity/fragment.pdb')
+   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 option, which, for 
@@ -58,7 +58,7 @@ This will group the atoms by residue. And, for completeness, we will first group
 
 .. code-block:: python
 
-  for chain in fragments.chains:
+  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).'
@@ -75,17 +75,16 @@ what bonds we have in there:
     
 From these short code examples we already see how the entity is structured: On 
 one hand we have a hierarchy of chains, residues and atoms. On the other hand, 
-we have bonds that form a network overlayed on the hierarchy. This is 
-illustrated in the picture on the left. An important feature of entities is that 
-we can always assume that the hierarchy is intact. You will never find an atom 
-without residues, no residue can exist without a parent chain and chains belong 
-always to an entity. 
+we have bonds that form a network overlayed on the hierarchy. An important 
+feature of entities is that we can always assume that the hierarchy is intact. 
+You will never find an atom without residues, no residue can exist without a 
+parent chain and chains belong always to an entity. 
 
 Let There Be Shiny Graphics
 --------------------------------------------------------------------------------
 
 For visually inspecting the fragment, we now create a graphical representation 
-of the entity. The graphical representation os 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.
+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
   
@@ -96,8 +95,8 @@ of the entity. The graphical representation os completely separate from the :cla
 
 Now you will see the fragment in the 3D window.
 
-Use the mouse to rotate, zoom in an shift the camera. Double clicking on an atom 
-will center the camera on that atom. If you want to learn more about the 
+Use the mouse to rotate, zoom in an 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`.