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University of Illinois at Urbana-Champaign

Beckman Institute for Advanced Science and Technology

Theoretical and Computational Biophysics Group

Computational Biophysics Workshop

Using VMD

VMD Developer:

John E. Stone

Tutorial Contributors:

Alek Aksimentiev, Anton Arkhipov, Reuven Birnbaum,

Robert Brunner, Jordi Cohen, Brijeet Dhaliwal, John Eargle,

Jen Hsin, Fatemeh Khalili, Eric H. Lee, Zan Luthey-Schulten,

Patrick O’Donoghue, Elijah Roberts, Anurag Sethi, Marcos So-

tomayor, John E. Stone, Emad Tajkhorshid, Leonardo Trabuco,

Elizabeth Villa, Yi Wang, David Wells, Dan Wright, Ying Yin

Apr. 2017

A current version of this tutorial is available at:

http://www.ks.uiuc.edu/Training/Tutorials/

Join the tutorial-l@ks.uiuc.edu mailing list for additional help.

CONTENTS 2

Contents

1 Working with a Single Molecule 7

1.1 Loading a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.2 Displaying the Molecule . . . . . . . . . . . . . . . . . . . . . . . 8

1.3 Graphical Representations . . . . . . . . . . . . . . . . . . . . . . 9

1.3.1 Exploring diﬀerent drawing styles . . . . . . . . . . . . . . 9

1.3.2 Exploring diﬀerent coloring methods . . . . . . . . . . . . 11

1.3.3 Displaying diﬀerent selections . . . . . . . . . . . . . . . . 12

1.3.4 Creating multiple representations . . . . . . . . . . . . . . 13

1.4 Sequence Viewer Extension . . . . . . . . . . . . . . . . . . . . . 15

1.5 Saving Your Work . . . . . . . . . . . . . . . . . . . . . . . . . . 16

1.6 The Basics of VMD Figure Rendering . . . . . . . . . . . . . . . 17

1.6.1 Setting the display background . . . . . . . . . . . . . . . 17

1.6.2 Increasing resolution . . . . . . . . . . . . . . . . . . . . . 17

1.6.3 Colors and materials . . . . . . . . . . . . . . . . . . . . . 18

1.6.4 Depth perception . . . . . . . . . . . . . . . . . . . . . . . 20

1.6.5 Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

2 Trajectories and Movie Making 25

2.1 Loading Trajectories . . . . . . . . . . . . . . . . . . . . . . . . . 25

2.2 Main Menu Animation Tools . . . . . . . . . . . . . . . . . . . . 26

2.3 Trajectory Visualization . . . . . . . . . . . . . . . . . . . . . . . 27

2.3.1 Smoothing trajectories . . . . . . . . . . . . . . . . . . . . 27

2.3.2 Displaying multiple frames . . . . . . . . . . . . . . . . . 27

2.3.3 Updating selections . . . . . . . . . . . . . . . . . . . . . 28

2.4 The Basics of Move Making in VMD . . . . . . . . . . . . . . . . 29

2.4.1 Making single-frame movies . . . . . . . . . . . . . . . . . 30

2.4.2 Making trajectory movies . . . . . . . . . . . . . . . . . . 30

3 Scripting in VMD 32

3.1 The Basics of Tcl Scripting . . . . . . . . . . . . . . . . . . . . . 32

3.2 VMD scripting . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

3.2.1 Loading molecules with text commands . . . . . . . . . . 34

3.2.2 The atomselect command . . . . . . . . . . . . . . . . . 35

3.2.3 Obtaining and changing molecule properties with text

commands . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

3.2.4 Sourcing scripts . . . . . . . . . . . . . . . . . . . . . . . . 39

3.3 Drawing shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

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