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pdbviewer's Introduction

Protein Data Bank (PDB) Viewer

Visualization of proteins directly from the PDB database or from a .pdb file.

Visualization example with protein 13PK:

Ball and Stick Backbone Space-Filling Ribbon Cartoon
CPK CPK - Ball and Stick CPK - Backbone CPK - Space-Filling CPK - Ribbon CPK - Cartoon
Structure Structure - Ball and Stick Structure - Backbone Structure - Space-Filling Structure - Ribbon Structure - Cartoon
Shapely Shapely - Ball and Stick Shapely - Backbone Shapely - Space-Filling Shapely - Ribbon Shapely - Cartoon
Sequence Sequence - Ball and Stick Sequence - Backbone Sequence - Space-Filling Sequence - Ribbon Sequence - Cartoon
Temperature Temperature - Ball and Stick Temperature - Backbone Temperature - Space-Filling Temperature - Ribbon Temperature - Cartoon

Overview over the whole PDB viewer:

PDB viewer overview

Features

  • Load list of proteins from the RCSB PDB RESTful Web Service interface
  • Load protein data in the Protein Data Bank (PDB) format from RCSB
  • Save protein data as .pdb file
  • Load protein data from a .pdb file
  • Color modes:
  • Styles
    • Ball and Stick
    • Backbone
    • Space-Filling
    • Ribbon
    • Cartoon
  • Change background color
  • Proportional atom radius (only for Ball and Stick, Backbone and Ribbon style)
  • Side chain connections in Ball and Stick style
  • Protein sequence and secondary structure in text fields
  • Mark / highlight atoms of amino acids in the protein graph and the sequence fields (except in the Cartoon style)
  • Rotate 3D protein graph around its center
  • Zoom in and out
  • Show simple statistics about the protein
  • Filter list of proteins by PDB id, classification and title

Requirements

  • Internet connection to initially load and to update the protein list
  • Internet connection to load protein data from RCSB
  • Java 1.8+

Contribution

Feel free to submitting issues and pull requests.

Authors

  • Sebastian Penhouët - Initial work - Spenhouet

License

This project is licensed under the MIT License - see the LICENSE file for details

Acknowledgments

pdbviewer's People

Contributors

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Watchers

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