Protein visualization and analysis with VMD


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This tutorial provides a short introduction to basic use of the VMD (“Visual Molecular Dynamics”) software to visualize and analyze proteins and molecular dynamics trajectories. It is part of the ASU course PHY 542/NAN 542 — Topics in Biophysics I.

For background on using VMD, look at [Hsin2008] and the official VMD tutorial. We will use data from the Protein Databank and [Beckstein2009].

Basics of protein structure are illustrated in [BrandenTooze] and in the lecture notes.


We are going to work through the individual sections in order. Use the navigation links in menu bar to move forward and backwards.

Learning Objectives

  • basic understanding of protein structure
  • familiarize with a molecular graphics program (VMD)
  • loading of static structures and dynamics trajectories
  • viewing a molecule (mouse, view modes)
  • representations
  • selections
  • making images
  • basic analysis
  • use of RMSFitting tools


[BrandenTooze]C. Branden and J. Tooze. Introduction to Protein Structure. 2nd ed, 1999, Garland Publishing, New York.
[Hsin2008]J. Hsin, A. Arkhipov, Y. Yin, J. E. Stone, and K. Schulten. Using VMD: An Introductory Tutorial, volume 24, chapter 5.7, pages 5.7.1–5.7.48. John Wiley & Sons, Inc., 2008. URL
[Beckstein2009]O Beckstein. EJ Denning, JR Perilla, and TB Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open/Closed Transitions. J Mol Biol 394 (2009), 160–176.

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