Protein Structure and PyMol

The aim of this practical is to ensure you have a good understanding of protein structure and that you understand the power of using protein structure to examine the effects of mutations. In particular you will:

  1. Learn the basic use of the PyMol molecular graphics program to examine protein structure
  2. Study phi and psi torsion angles and the Ramachandran plot
  3. Identify structural features such as the active and binding sites of an enzyme
  4. Map mutations onto protein structure to understand their possible effects on protein function

This web-based practical will guide you through using PyMol - a molecular graphics program - to examine protein structures. You will also look at some Bioinformatics resources to obtain protein sequence related data and mutation information.

Throughout the tutorial we are going to focus on two proteins:


Throughout the practical, the aim of what you are trying to do is shown like this. Make sure you read this before proceeding, to ensure you understand the purpose behind the next steps.

Throughout the practical, important notes are shown like this.

Throughout the practical, specific instructions are shown like this.

Warning! You must record information as you go along where instructed to do so. This will enable you to answer the questions in the quiz at the end of the tutorial.

When you need to record information it will be highlighted like this.

When you complete the quiz, you will be asked to enter your name and email address to confirm that you have completed the tutorial.