vmd-tutorial - University of Illinois at Urbana-Champaign...

Info iconThis preview shows pages 1–4. Sign up to view the full content.

View Full Document Right Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: 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 Stone Tutorial Contributors: Alek Aksimentiev, Anton Arkhipov, Robert Brunner, Jordi Cohen, Brijeet Dhaliwal, John Eargle, Jen Hsin, Fatemeh Khalili, Eric H. Lee, Zan Luthey-Schulten, Patrick ODonoghue, Elijah Roberts, Anurag Sethi, Marcos Sotomayor, Emad Tajkhorshid, Leonardo Trabuco, Elizabeth Villa, Yi Wang, David Wells, Dan Wright, Ying Yin July 2009 2 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 3 Contents 1 Working with a Single Molecule 8 1.1 Loading a Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.2 Displaying the Molecule . . . . . . . . . . . . . . . . . . . . . . . 9 1.3 Graphical Representations . . . . . . . . . . . . . . . . . . . . . . 10 1.3.1 Exploring different drawing styles . . . . . . . . . . . . . . 10 1.3.2 Exploring different coloring methods . . . . . . . . . . . . 12 1.3.3 Displaying different selections . . . . . . . . . . . . . . . . 13 1.3.4 Creating multiple representations . . . . . . . . . . . . . . 14 1.4 Sequence Viewer Extension . . . . . . . . . . . . . . . . . . . . . 15 1.5 Saving Your Work . . . . . . . . . . . . . . . . . . . . . . . . . . 17 1.6 The Basics of VMD Figure Rendering . . . . . . . . . . . . . . . 18 1.6.1 Setting the display background . . . . . . . . . . . . . . . 18 1.6.2 Increasing resolution . . . . . . . . . . . . . . . . . . . . . 18 1.6.3 Colors and materials . . . . . . . . . . . . . . . . . . . . . 19 1.6.4 Depth perception . . . . . . . . . . . . . . . . . . . . . . . 21 1.6.5 Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 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 . . . . . . . . . . . . . . . . . . . . . . . . . . .commands ....
View Full Document

This note was uploaded on 01/06/2010 for the course PHYSICS 4500 taught by Professor J during the Spring '09 term at Missouri (Mizzou).

Page1 / 68

vmd-tutorial - University of Illinois at Urbana-Champaign...

This preview shows document pages 1 - 4. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online