.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/gallery/structure/misc/homolog_superimposition.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_misc_homolog_superimposition.py>`
        to download the full example code

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

.. _sphx_glr_examples_gallery_structure_misc_homolog_superimposition.py:


Superimposition of homologous protein structures
================================================

This script superimposes the structure of a streptavidin monomer
into an avidin monomer.
The visualization was conducted with PyMOL.

- *Green*:  Avidin
- *Orange*: Strepatvidin

.. GENERATED FROM PYTHON SOURCE LINES 12-36



.. image-sg:: /examples/gallery/structure/misc/images/sphx_glr_homolog_superimposition_001.png
   :alt: homolog superimposition
   :srcset: /examples/gallery/structure/misc/images/sphx_glr_homolog_superimposition_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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

    import biotite.database.rcsb as rcsb
    import biotite.structure as struc
    import biotite.structure.io.pdbx as pdbx


    def _extract_monomer(complex):
        complex = complex[struc.filter_amino_acids(complex)]
        # Get the monomer that belongs to the first atom in the structure
        return complex[struc.get_chain_masks(complex, [0])[0]]


    avidin_file = pdbx.BinaryCIFFile.read(rcsb.fetch("1vyo", "bcif"))
    avidin = _extract_monomer(pdbx.get_structure(avidin_file, model=1, include_bonds=True))
    streptavidin_file = pdbx.BinaryCIFFile.read(rcsb.fetch("6j6j", "bcif"))
    streptavidin = _extract_monomer(
        pdbx.get_structure(streptavidin_file, model=1, include_bonds=True)
    )

    streptavidin, _, _, _ = struc.superimpose_homologs(avidin, streptavidin)
    # Visualization with PyMOL...


.. _sphx_glr_download_examples_gallery_structure_misc_homolog_superimposition.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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