Identify secondary structure and topology
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Sketch a topology diagram on paper (use open structure for analysis):
  
  - number helices H1 - H8 (ignore short < 4 res, count all helices as
    helix, alpha, pi, 3-10)

  - sheets A, B, C, number strands SA1-SA5, SB1-3, SC1-2

  - start with central b-sheet
  
  - 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`_ in the user manual for details.

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


.. figure:: /images/adk-topolo.*

   Topology diagram of AdK.


.. _selections: http://www.ks.uiuc.edu/Research/vmd/current/ug/node88.html#ug:topic:selections