.. -*- coding: utf-8 -*-

.. |->| replace:: →

===========================================
 Identify secondary structure and topology
===========================================

Sketch a topology diagram on paper (use the open structure `4AKE`_ for
analysis):
  
- number helices **H1 - H8** (ignore short helices < 4 residues, count all
  helices as helix (:math:`\alpha`-helix, :math:`\pi`-helix ,
  :math:`3_{10}`-helix))

- label the :math:`\beta`-sheets **A, B, C**, number individual
  strands **A1-A5**, **B1-B2**, **C1-C3**

- start with the central :math:`\beta`-sheet as A

- locate N-terminus (resid 1 and name CA, color blue, VDW) and C terminus

  .. note:: 

    You can do ranges: ``resid 1 to 5`` or multiple ranges: ``resid
    1 to 5 20 to 50``. 

    You can use boolean operators ``and``, ``or``, ``not``. See
    **Selections Tab** and **Selection Methods** in the `user manual`_
    for details.

- draw connections between secondary elements in your topology
  diagram and label secondary structure elements.


.. figure:: /images/adk-topology-incomplete.*

   Left: Structure of AdK in its open conformation, colored by
   secondary structure elements. Right: Incomplete topology diagram of AdK.


.. _user manual: http://www.ks.uiuc.edu/Research/vmd/current/ug/
.. _4AKE: http://www.rcsb.org/pdb/explore/explore.do?pdbId=4AKE