.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/gallery/structure/ramachandran.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_gallery_structure_ramachandran.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_gallery_structure_ramachandran.py:


Ramachandran plot of dynein motor domain
========================================

This script creates a Ramachandran plot
of the motor domain of dynein (PDB: 3VKH).
The protein mainly consists of alpha-helices,
as the plot clearly indicates.

.. GENERATED FROM PYTHON SOURCE LINES 10-52



.. image-sg:: /examples/gallery/structure/images/sphx_glr_ramachandran_001.png
   :alt: Ramachandran plot of dynein motor domain
   :srcset: /examples/gallery/structure/images/sphx_glr_ramachandran_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    # Code source: Patrick Kunzmann
    # License: BSD 3 clause

    from tempfile import gettempdir
    import biotite.structure as struc
    import biotite.structure.io as strucio
    import biotite.database.rcsb as rcsb
    import matplotlib.pyplot as plt
    import numpy as np
    from matplotlib import colors
    import scipy.stats as sts

    # Download and parse file
    file = rcsb.fetch("3vkh", "cif", gettempdir())
    atom_array = strucio.load_structure(file)
    # Calculate backbone dihedral angles
    # from one of the two identical chains in the asymmetric unit
    phi, psi, omega = struc.dihedral_backbone(
        atom_array[atom_array.chain_id == "A"]
    )
    # Conversion from radians into degree
    phi *= 180/np.pi
    psi *= 180/np.pi
    # Remove invalid values (NaN) at first and last position
    phi= phi[1:-1]
    psi= psi[1:-1]

    # Plot density
    figure = plt.figure()
    ax = figure.add_subplot(111)
    h, xed, yed, image = ax.hist2d(phi, psi, bins=(200, 200),
                    cmap="RdYlGn_r", cmin=1)
    cbar = figure.colorbar(image, orientation="vertical")
    cbar.set_label("Count")
    ax.set_aspect("equal")
    ax.set_xlim(-180, 175)
    ax.set_ylim(-180, 175)
    ax.set_xlabel(r"$\phi$")
    ax.set_ylabel(r"$\psi$")
    ax.set_title("Ramachandran plot of dynein motor domain")
    figure.tight_layout()
    plt.show()

.. _sphx_glr_download_examples_gallery_structure_ramachandran.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: ramachandran.ipynb <ramachandran.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: ramachandran.py <ramachandran.py>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_