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Molecular Visualization Using PyMOL: Home

Using PyMOL to view, create, and render informative figures of biomolecules for research, teaching, and learning.

PyMOL Introduction

PyMOL is a molecular visualization software program used for modeling and visualizing 3D structures of biomolecules (proteins, DNA, RNA, lipids, small molecules, etc.). Using PyMOL, it is possible to make high-quality images (renders) of molecules suited for publications. There are a variety of tools and ways to use PyMOL. Some examples are below:


                            PDB ID: 2BDA - Porcine Pancreatic Elastase                           PDB ID: 4PRG - Peroxisome Proliferated-Activated Receptor (PPAR) Gamma  

Linked below are tutorials on PyMOL that vary from the basics of the User Interface (UI), to how to make elaborate movies with multiple structures, to advanced features on aligning, surface rendering, and more. These tutorials are available in a written or video format.


Virginia Tech Faculty, Staff, and Students can download licensed PyMOL via VT ITPALS Software Service Center


The first written and video tutorial (1 - Introduction) linked below also details how to download PyMOL for Virginia Tech Faculty, Staff, and Students with the VT site license. 


Have questions about PyMOL? Want to integrate it into your classroom or research project?

Contact Anne M. Brown ( for more information. 

Special thanks to DataBridge undergrad research student Carter Gottschalk (VT Biology, 2020) for working on these tutorials and videos to support molecular visualization at VT! 

PyMOL Tutorials

1. Introduction/User Interface of PyMOL

This tutorial outlines the installation of PyMOL and introduces the user to the scope and use for PyMOL. The user interface (UI) is explored and a simple render of a protein is created. This tutorial is for anyone using PyMOL for the first time or needing a refresher to version 2.3+. 

For more information about PyMOL or for questions not covered here, see the PyMOL support page

Interested in learning more about Molecular Visualization? More tutorials available at the Bevan Brown Lab Open Science Framework

Check out the Wiki pages on the OSF for more tutorials and updates. We will also post more tutorial links here as they are created. 


Science Informatics Consultant and Health Analytics Coordinator

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Anne Brown
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