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Visualizing Proteins Using PyMOL Software

Workshop Code (B7)

Visualizing proteins using PyMOL software

This workshop provides an introduction to the fundamentals of utilizing PyMOL, a protein visualization software. Being among the early freely available programs online, PyMOL can be operated using code or a graphical user interface (GUI). Users can import protein structures from the Protein Data Bank (PDB) and visualize them in PyMOL. The software enables users to view protein structures in various forms (stick, cartoon, helix, etc.), apply different colors to subunits/molecules/amino acids/chains, perform amino acid mutations, inspect the protein’s surface charge, and much more.


  • 9:30 AM – 11:00 AM:Introduction to protein structure and the main components to be seen in a protein
  • 11:00 AM – 12:30 PM:How to navigate a structure in PyMOL (basic skills)
  • 12:30 PM – 1:00 PM: Break
  • 1:00 PM – 4:00 PM: Hands-on activity: Importing a protein from the PDB database and visualizing in PyMOL


  • 9:30 AM – 11:00 AM: How to use PyMOL for analyzing different structural features of a protein
  • 11:00 AM – 12:30 PM: Questions and Answers
  • 12:30 PM – 1:00 PM: Break
  • 1:00 PM – 4:00 PM: Hands-on activity: Manipulation of protein structure in PyMOL

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