.. _sphx_glr_examples_gallery_structure:

Structures
----------


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    <div class="sphx-glr-thumbnails">


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example we create an adjacency matrix of the CA atoms in the lysozyme crystal structure...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_adjacency_matrix_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_adjacency_matrix.py`

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      <div class="sphx-glr-thumbnail-title">Construction of an adjacency matrix</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The purpose of this example is to demonstrate the capabilities of the PubChem interface. As a t...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_alkane_isomers_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_alkane_isomers.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Enumeration of alkane isomers</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example we plot a linear secondary-structure diagram of a tRNA mimic (PDB ID: 4P5J) fro...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_base_pairs_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_base_pairs.py`

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      <div class="sphx-glr-thumbnail-title">Plotting the base pairs of a tRNA-like-structure</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Often the biological assembly (or biological unit) reveals the complete picture of a protein fu...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_biological_assembly_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_biological_assembly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Biological assembly of a structure</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This script identifies which amino acids of the phage 434 repressor are in contact with its cor...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_contact_sites_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_contact_sites.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Contact sites of protein-DNA interaction</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script calculates the diameter of a protein defined as the maximum pairwise atom distance.">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_diameter_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_diameter.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Calculation of protein diameter</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example presents a function that detects disulfide bridges in protein structures. Then the...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_disulfide_bonds_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_disulfide_bonds.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Detection of disulfide bonds</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use AutoDock Vina Trott2010 from within Biotite for docking a ligand ...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_docking_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_docking.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Docking biotin to streptavidin</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example we will identify the hydrogen bonds between the p-Helix and the selecivity filt...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_domain_hbonds_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_domain_hbonds.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Hydrogen bonds between protein domains</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script creates two bars, each indicating gaps in the structure of DNA-PKcs. The top bar in...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_gap_bars_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_gap_bars.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Missing residues in protein structures of DNA-PKcs</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example we will visualize the glycosylation of amino acid residues in an arbitrary prot...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_glycan_visualization_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_glycan_visualization.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Visualization of glycosylated amino acids</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script superimposes the atom coordinates of the Ku70/80 heterodimer onto the corresponding...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_ku_superimposition_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_ku_superimposition.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Superimposition of two protein structures</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script implements the LeafletFinder algorithm Michaud-Agrawal2011 used by MDAnalysis. The ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_leaflet_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_leaflet.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Identification of lipid bilayer leaflets</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example we plot a secondary structure diagram annotated with  Leontis-Westhof nomenclat...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_leontis_westhof_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_leontis_westhof.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Leontis-Westhof Nomenclature</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we will analyze a trajectory of a Gromacs MD simulation: The trajectory contai...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_md_analysis_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_md_analysis.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Basic analysis of a MD simulation</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how the BinaryCIF format can be used as an alternative to classical t...">

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  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_mmtf_trajectory_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_mmtf_trajectory.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">BinaryCIF as trajectory format</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Biotite provides simple interactive molecular visualization via plot_atoms(). Although it does ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_molecular_visualization_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_molecular_visualization.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Molecular visualization of caffeine</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The elastic network model (ENM) is a fast method to estimate movements in a protein structure, ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_normal_modes_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_normal_modes.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Visualization of normal modes from an elastic network model</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example we perform a structural alignment of multiple lysozyme variants from different ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_pb_alignment_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_pb_alignment.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Structural alignment of lysozyme variants using 'Protein Blocks'</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script creates a plot showing the number of annually released PDB structures since 1990, v...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_pdb_statistics_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_pdb_statistics.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Annual releases of PDB structures</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This examples shows how partial charges are distributed in a small molecule. The charges are ca...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_peoe_visualization_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_peoe_visualization.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Partial charge distribution</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script presents a function that takes an amino acid sequence and builds a straight peptide...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_peptide_assembly_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_peptide_assembly.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Assembly of a straight peptide from sequence</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script creates a Ramachandran plot of the motor domain of dynein (PDB: 3VKH). The protein ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_ramachandran_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_ramachandran.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Ramachandran plot of dynein motor domain</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script determines whether a protein structure contains L- or D-amino acids. D-amino acids ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_residue_chirality_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_residue_chirality.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Determination of amino acid enantiomers</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script creates rotamers for an amino acid, by randomly rotating about all rotatable bonds....">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_rotamer_library_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_rotamer_library.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Creation of an amino acid rotamer library</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This scripts plots the arrangements of strands in selected β-sheets of a protein structure. The...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_sheet_arrangement_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_sheet_arrangement.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Arrangement of beta-sheets</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Based on a 10 ns Gromacs MD simulation of 0.15 mM sodium chloride, the distance of solvation sh...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_solvation_shells_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_solvation_shells.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Solvation shells of sodium and chloride ions</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script displays positional changes of secondary structure elements (SSE) in the course of ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_trajectory_sse_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_trajectory_sse.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Secondary structure during an MD simulation</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example we plot a secondary-structure diagram of a tRNA mimic  (PDB ID: 4P5J) from the ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_transfer_rnas_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_transfer_rnas.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Comparison of a tRNA-like-structure with a tRNA</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we will obtain the secondary structure of the transketolase crystal structure ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_transketolase_sse_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_transketolase_sse.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Three ways to get the secondary structure of a protein</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In selective sodium/potassium channels, the internal cavity of the pore is walled off from the ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_water_exchange_noexec_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_water_exchange_noexec.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Cavity solvation in different states of HCN4</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This script displays the adenine-thymine and guanine-cytosine base pairs, taken from an actual ...">

.. only:: html

  .. image:: /examples/gallery/structure/images/thumb/sphx_glr_watson_crick_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_watson_crick.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Visualization of Watson-Crick base pairs</div>
    </div>


.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/gallery/structure/adjacency_matrix
   /examples/gallery/structure/alkane_isomers
   /examples/gallery/structure/base_pairs
   /examples/gallery/structure/biological_assembly
   /examples/gallery/structure/contact_sites
   /examples/gallery/structure/diameter
   /examples/gallery/structure/disulfide_bonds
   /examples/gallery/structure/docking
   /examples/gallery/structure/domain_hbonds
   /examples/gallery/structure/gap_bars
   /examples/gallery/structure/glycan_visualization
   /examples/gallery/structure/ku_superimposition
   /examples/gallery/structure/leaflet
   /examples/gallery/structure/leontis_westhof
   /examples/gallery/structure/md_analysis
   /examples/gallery/structure/mmtf_trajectory
   /examples/gallery/structure/molecular_visualization
   /examples/gallery/structure/normal_modes
   /examples/gallery/structure/pb_alignment
   /examples/gallery/structure/pdb_statistics
   /examples/gallery/structure/peoe_visualization
   /examples/gallery/structure/peptide_assembly
   /examples/gallery/structure/ramachandran
   /examples/gallery/structure/residue_chirality
   /examples/gallery/structure/rotamer_library
   /examples/gallery/structure/sheet_arrangement
   /examples/gallery/structure/solvation_shells
   /examples/gallery/structure/trajectory_sse
   /examples/gallery/structure/transfer_rnas
   /examples/gallery/structure/transketolase_sse
   /examples/gallery/structure/water_exchange_noexec
   /examples/gallery/structure/watson_crick