Next: Introduction

University of Illinois at Urbana-Champaign
Beckman Institute for Advanced Science and Technology
Theoretical and Computational Biophysics Group
Biophysics 590C: Fall 2004

VMD Molecular Graphics

VMD Developer: John Stone
Jordi Cohen Marcos Sotomayor Elizabeth Villa September 2004.

- Introduction
  - Getting Started
- Basics of VMD
  - Loading a Molecule
  - Displaying the Protein
  - Exploring Different Drawing Styles
  - Exploring Different Coloring Methods
  - Exploring Different Selections
  - Multiple Representations
  - Sequence Viewer Extension
  - Saving your Work
- Multiple Molecules and Scripting
  - Loading Multiple Molecules
  - Using the Main Window
  - Tcl Scripting Basics and Tk Console
  - The `atomselect` Command
  - Aligning Two Molecules
  - Using Color to Display the Deviation
- Trajectories, Macros and Labels
  - Loading trajectories
  - Macros
  - Main Menu Animation Tools
  - Labels
  - An Example Tcl Script: Calculating the RMSD of a trajectory