diff --git a/package/doc/sphinx/source/documentation_pages/advanced_reader.rst b/package/doc/sphinx/source/documentation_pages/advanced_reader.rst
new file mode 100644
index 00000000000..babde3da7a5
--- /dev/null
+++ b/package/doc/sphinx/source/documentation_pages/advanced_reader.rst
@@ -0,0 +1,7 @@
+.. -*- coding: utf-8 -*-
+
+.. All the advanced options in Reader usage and creation
+
+chainreader
+
+auxiliaries
diff --git a/package/doc/sphinx/source/documentation_pages/advanced_topology.rst b/package/doc/sphinx/source/documentation_pages/advanced_topology.rst
new file mode 100644
index 00000000000..9d849c2720f
--- /dev/null
+++ b/package/doc/sphinx/source/documentation_pages/advanced_topology.rst
@@ -0,0 +1,5 @@
+.. -*- coding: utf-8 -*-
+
+.. Manipulating the Topology object and TopologyAttrs
+
+Adding custom topology attrs
diff --git a/package/doc/sphinx/source/documentation_pages/advanced_universe.rst b/package/doc/sphinx/source/documentation_pages/advanced_universe.rst
new file mode 100644
index 00000000000..fa91b23b2be
--- /dev/null
+++ b/package/doc/sphinx/source/documentation_pages/advanced_universe.rst
@@ -0,0 +1,5 @@
+.. -*- coding: utf-8 -*-
+
+.. All the advanced options in Universe creation
+
+transfer to memory
diff --git a/package/doc/sphinx/source/documentation_pages/bonds_angles_torsions.rst b/package/doc/sphinx/source/documentation_pages/bonds_angles_torsions.rst
new file mode 100644
index 00000000000..0ca5b2511e0
--- /dev/null
+++ b/package/doc/sphinx/source/documentation_pages/bonds_angles_torsions.rst
@@ -0,0 +1,12 @@
+.. -*- coding: utf-8 -*-
+
+.. working with bonds angles and torsions
+
+
+Getting them
+
+TopologyGroups
+
+Selecting them (select_bonds)
+
+Intersections
diff --git a/package/doc/sphinx/source/documentation_pages/coordinate_manipulation.rst b/package/doc/sphinx/source/documentation_pages/coordinate_manipulation.rst
new file mode 100644
index 00000000000..6a45020e06f
--- /dev/null
+++ b/package/doc/sphinx/source/documentation_pages/coordinate_manipulation.rst
@@ -0,0 +1,20 @@
+.. -*- coding: utf-8 -*-
+
+.. Working with coordinates and things specific to MDA
+   Maybe a basic overview of numpy arrays, but nothing too much
+   Mostly dealing with lib.distances and ways to abuse it!
+
+Reminder on how to get position data
+
+Basics of numpy arrays
+
+lib.distances
+- distance_array
+- self_distance_array
+- calc_bonds
+- calc_angles
+- calc_torsions
+
+Periodic boundary conditions
+
+pack_into_box
diff --git a/package/doc/sphinx/source/documentation_pages/working_with_atomgroups.rst b/package/doc/sphinx/source/documentation_pages/working_with_atomgroups.rst
new file mode 100644
index 00000000000..b3791e98ad3
--- /dev/null
+++ b/package/doc/sphinx/source/documentation_pages/working_with_atomgroups.rst
@@ -0,0 +1,14 @@
+.. -*- coding: utf-8 -*-
+.. All about how to use AtomGroups
+   very basic as this is one of the first topics in
+   the quasi tutorial
+
+Slicing
+
+Adding
+
+Common attributes
+
+Common methods
+
+Show their use in functions?
diff --git a/package/doc/sphinx/source/documentation_pages/working_with_residues.rst b/package/doc/sphinx/source/documentation_pages/working_with_residues.rst
new file mode 100644
index 00000000000..cf8f3eb2588
--- /dev/null
+++ b/package/doc/sphinx/source/documentation_pages/working_with_residues.rst
@@ -0,0 +1,20 @@
+.. -*- coding: utf-8 -*-
+
+.. AtomGroups have been introduced, now introduce the idea of a
+   hierarchy of different levels
+
+Describe the membership rules, each atom belongs to one and only one
+Residue, same with Res to Segment
+
+Residue and Segment attributes
+
+Make it clear that some attributes must be accessed via further
+shortcuts, ie Residue.atoms.masses
+
+Make it clear that some attributes 'belong' to a level,
+ie Atom.resid belongs only to the Residue and can't fall
+out of sync.
+
+Residue and Segment methods
+
+Moving between Residues and Segments
diff --git a/package/doc/sphinx/source/documentation_pages/working_with_trajectories.rst b/package/doc/sphinx/source/documentation_pages/working_with_trajectories.rst
new file mode 100644
index 00000000000..9ae460e9120
--- /dev/null
+++ b/package/doc/sphinx/source/documentation_pages/working_with_trajectories.rst
@@ -0,0 +1,15 @@
+.. -*- coding: utf-8 -*-
+
+.. Working with the Reader object
+   There is also an advanced version of this, so anything complicated
+   can be deferred to there.
+
+AtomGroup access to the trajectory
+
+One frame at a time policy
+
+Trajectory manipulation, ie iteration and seeking
+
+The timestep object
+
+Timestep object attributes (time, dt, others)
diff --git a/package/doc/sphinx/source/index.rst b/package/doc/sphinx/source/index.rst
index 27b33473d65..0fbd36622bd 100644
--- a/package/doc/sphinx/source/index.rst
+++ b/package/doc/sphinx/source/index.rst
@@ -67,16 +67,33 @@ literature. Please make sure to also reference any
 Thank you!
 
 
-Contents
-========
+MDAnalysis Basics
+=================
 
 .. toctree::
    :maxdepth: 1
-   :numbered:		
-   
+   :numbered:
+
    ./documentation_pages/overview
    ./documentation_pages/topology
+   ./documentation_pages/working_with_atomgroups
    ./documentation_pages/selections
+   ./documentation_pages/working_with_residues
+   ./documentation_pages/working_with_trajectories
+   ./documentation_pages/coordinate_manipulation
+   ./documentation_pages/bonds_angles_torsions
+   ./documentation_pages/advanced_universe
+   ./documentation_pages/advanced_reader
+   ./documentation_pages/advanced_topology
+
+
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 1
+   :numbered:		
+   
    ./documentation_pages/analysis_modules
    ./documentation_pages/topology_modules
    ./documentation_pages/coordinates_modules