.. _sphx_glr_examples_gallery_structure:
Structures
----------
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_adjacency_matrix_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_adjacency_matrix.py`
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Construction of an adjacency matrix
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_alkane_isomers_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_alkane_isomers.py`
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Enumeration of alkane isomers
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_base_pairs_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_base_pairs.py`
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Plotting the base pairs of a tRNA-like-structure
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_biological_assembly_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_biological_assembly.py`
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Biological assembly of a structure
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_contact_sites_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_contact_sites.py`
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Contact sites of protein-DNA interaction
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_diameter_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_diameter.py`
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Calculation of protein diameter
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_disulfide_bonds_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_disulfide_bonds.py`
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Detection of disulfide bonds
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_docking_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_docking.py`
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Docking biotin to streptavidin
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_domain_hbonds_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_domain_hbonds.py`
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Hydrogen bonds between protein domains
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_gap_bars_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_gap_bars.py`
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Missing residues in protein structures of DNA-PKcs
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_glycan_visualization_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_glycan_visualization.py`
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Visualization of glycosylated amino acids
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_ku_superimposition_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_ku_superimposition.py`
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Superimposition of two protein structures
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_leaflet_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_leaflet.py`
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Identification of lipid bilayer leaflets
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_leontis_westhof_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_leontis_westhof.py`
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Leontis-Westhof Nomenclature
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_md_analysis_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_md_analysis.py`
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Basic analysis of a MD simulation
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_mmtf_trajectory_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_mmtf_trajectory.py`
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BinaryCIF as trajectory format
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_molecular_visualization_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_molecular_visualization.py`
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Molecular visualization of caffeine
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_normal_modes_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_normal_modes.py`
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Visualization of normal modes from an elastic network model
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_pb_alignment_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_pb_alignment.py`
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Structural alignment of lysozyme variants using 'Protein Blocks'
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_pdb_statistics_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_pdb_statistics.py`
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Annual releases of PDB structures
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_peoe_visualization_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_peoe_visualization.py`
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Partial charge distribution
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_peptide_assembly_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_peptide_assembly.py`
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Assembly of a straight peptide from sequence
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_ramachandran_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_ramachandran.py`
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Ramachandran plot of dynein motor domain
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_residue_chirality_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_residue_chirality.py`
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Determination of amino acid enantiomers
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_rotamer_library_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_rotamer_library.py`
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Creation of an amino acid rotamer library
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_sheet_arrangement_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_sheet_arrangement.py`
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Arrangement of beta-sheets
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_solvation_shells_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_solvation_shells.py`
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Solvation shells of sodium and chloride ions
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_trajectory_sse_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_trajectory_sse.py`
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Secondary structure during an MD simulation
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_transfer_rnas_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_transfer_rnas.py`
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Comparison of a tRNA-like-structure with a tRNA
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_transketolase_sse_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_transketolase_sse.py`
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Three ways to get the secondary structure of a protein
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_water_exchange_noexec_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_water_exchange_noexec.py`
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Cavity solvation in different states of HCN4
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.. image:: /examples/gallery/structure/images/thumb/sphx_glr_watson_crick_thumb.png
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:ref:`sphx_glr_examples_gallery_structure_watson_crick.py`
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Visualization of Watson-Crick base pairs
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.. 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