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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_gallery_normal_mode.py>`
        to download the full example code

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

.. _sphx_glr_examples_gallery_normal_mode.py:


Normal modes of a protein
=========================

This example script calculates the normal modes of an ANM and visualizes one
of them using arrows.

.. GENERATED FROM PYTHON SOURCE LINES 8-71



.. image:: /examples/gallery/images/sphx_glr_normal_mode_001.png
    :alt: normal mode
    :class: sphx-glr-single-img





.. code-block:: default


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

    import numpy as np
    import biotite.structure as struc
    import biotite.structure.io.mmtf as mmtf
    import biotite.database.rcsb as rcsb
    import ammolite
    import springcraft


    PNG_SIZE = (800, 800)


    PDB_ID = "1MUG"
    # The normal mode to be visualized
    # '6' is the slowest (most significant) one that does not correspond to
    # translation or rotation of the system
    MODE = 6
    # The maximum arrow length depicting the displacement
    # (The length of the ANM's eigenvectors make only sense when compared
    # relative to each other, the absolute values have no significance)
    AMPLITUDE = 10


    # Load structure
    mmtf_file = mmtf.MMTFFile.read(rcsb.fetch(PDB_ID, "mmtf"))
    structure = mmtf.get_structure(mmtf_file, model=1, include_bonds=True)

    # Filter first peptide chain
    protein_chain = structure[
        struc.filter_amino_acids(structure)
        & (structure.chain_id == structure.chain_id[0])
    ]
    # Filter CA atoms
    ca_mask = (protein_chain.atom_name == "CA") & (protein_chain.element == "C")
    ca = protein_chain[ca_mask]

    ff = springcraft.InvariantForceField(13.0)
    anm = springcraft.ANM(ca, ff)
    _, eigen_vectors = anm.eigen()
    vector = eigen_vectors[MODE].reshape(-1, 3)
    vector /= np.max(vector)
    vector *= AMPLITUDE


    ammolite.cmd.set("cartoon_oval_length", 1.0)
    pymol_object = ammolite.PyMOLObject.from_structure(protein_chain)
    pymol_object.show_as("cartoon")
    # Show eigenvectors as arrows
    ammolite.draw_arrows(
        ca.coord, ca.coord + vector,
        radius=0.2, head_radius=0.4, head_length=1.0
    )
    ammolite.cmd.set_view((
         0.605540633,    0.363677770,   -0.707855821,
        -0.416691631,    0.902691007,    0.107316799,
         0.678002179,    0.229972601,    0.698157668,
         0.000000000,    0.000000000, -115.912551880,
        32.098876953,   31.005725861,   78.377349854,
        89.280677795,  142.544403076,  -20.000000000
    ))
    ammolite.show(PNG_SIZE)

.. _sphx_glr_download_examples_gallery_normal_mode.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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