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

.. |->| replace:: →

.. _Secondary_structure:

==========================================
 Analyzing protein structure and topology
==========================================

We will use VMD_ ("Visual Molecular Dynamics") to learn more about a
protein. We use the enzyme adenylate kinase ("AdK") as an example
throughout.

For background on using VMD_, look at [Hsin2008]_ and the `VMD tutorial`_.


Topology and secondary structure
--------------------------------

In order to deduce the topology of the protein we will need to load
the experimental coordinates into VMD (stored in "structure" file in
the PDB format) and then use different representations to more clearly
see the underlying secondary and tertiary structural elements.


Load the protein structure
~~~~~~~~~~~~~~~~~~~~~~~~~~

Load AdK in its open conformation (PDB 4AKE_) and visualize its
topology and secondary structure:

- get *adk_open.pdb* from
  https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/files/
  or from the `Protein Databank`_ under accession code (PDB ID)
  4AKE_.

  Remember in which directory you saved it or better, put it into a
  dedicated folder for this tutorial.

- **load the coordinate file ("structure"):**
  :menuselection:`File --> New Molecule`    

  * :guilabel:`Load files for:` *New Molecule*
  * :guilabel:`Filename` (browse for your file)
  * :guilabel:`Determine file type`: *Automatically*

- settings in VMD (use these settings for all further exercises):

  * :menuselection:`Display --> Orthographic`
  * :menuselection:`Graphics --> Color: Display: Background: White`
  * *optional*: Try if :menuselection:`Display --> Rendermode --> GLSL`
    works for you.

    This *should* work with most modern graphics cards that are OpenGL
    capable. Once VMD uses OpenGL, it will render everything much
    faster and the results will look much smoother than with the
    standard (not accelerated) setting. However, if you cannot display
    certain representations (e.g., VDW) then unset this setting again.


Visualize a protein in cartoon representation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

We now want to look at the protein structure in more detail by using
different **representations** and **color**.

- :menuselection:`Graphics --> Representations`

  - :guilabel:`Selected Atoms:` *protein* (if you downloaded 4AKE_ from the PDB,
    use *protein and chain A*)
  - :guilabel:`Drawing Method:` *New Cartoon* representation,
  - :guilabel:`Coloring Method:` *Secondary Structure*

- you can add more representations and switch between them by clicking
  the representations in the list
  

Interacting with the visualization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- moving and rotating with the *mouse* (when in the *rotate* view
  mode)

  - left button: rotate X/Y
  - right button (or left + Command key on Mac): rotate Z

- keys to switch between different **view modes** (or use the
  :menuselection:`Mouse` menu)

  - :kbd:`r`: rotate
  - :kbd:`t`: translate
  - :kbd:`s`: scale
  - :kbd:`=`: reset view (not a mode but very useful), also
    :menuselection:`Display --> Reset View &=`

Exercises
---------

.. toctree::
   :maxdepth: 1

   topology
   ramachandran
   domains
   ligands
   summary
   

.. References
.. ----------

.. _VMD: http://www.ks.uiuc.edu/Research/vmd

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

.. _VMD tutorial: http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/

.. _1AKE: http://www.rcsb.org/pdb/explore/explore.do?pdbId=1AKE
.. _1AKE pdb: http://doi.org/10.2210/pdb1ake/pdb

.. _4AKE: http://www.rcsb.org/pdb/explore/explore.do?pdbId=4AKE
.. _4AKE pdb: http://doi.org/10.2210/pdb4ake/pdb

.. _Protein Databank: http://www.rcsb.org/pdb/