CDK2 Ramachandran
=================

1. Make a Ramachandran plot of all residues in all chains. Classify each residue by phi/psi combination as defined in North, B.;  Lehmann, A.;  Dunbrack, R. L. Journal of Molecular Biology 2011, 406, 228-256. Contours are at Fibonacci numbers.

.. code-block:: sh

    polyphony_plot_Ramachandran.py -f clust_1HCK_A_95.fasta -p phipsi
    

.. image:: images/cdk2/phi-psi.png
    :scale: 25 %
    :align: center

2. Plot a scatter plot of curvature against torsion for every c-alpha atom in all chains, coloured by region of the Ramachandran plot. 

.. code-block:: sh

    polyphony_plot_Ramachandran.py -f clust_1HCK_A_95.fasta


.. image:: images/cdk2/curvature-torsion.png
    :scale: 25 %
    :align: center

3. View in 3D in PyMol. Start pymol -R and in another window a ipython session

.. code-block:: python

    from Polyphony.Pymol import Pymol_Viz
    cdk2 = Pymol_Viz("clust_1HCK_A_95.fasta","cdk2")
    
    # Colour by torsion
    cdk2.colour_single_structure_property(property="backbone", dimension=0)
    
    # Duplicate object in Pymol. Then colour by curvature.
    cdk2.colour_single_structure_property(property="backbone", dimension=1)
    
    # Duplicate object in Pymol. Then colour by Ramachandran region (same as 2D plot above)
    cdk2.colour_by_Ramachandran_region()


.. image:: images/cdk2/back_conf_3d.png
    :scale: 25 %
    :align: center