List of Figures

1. Sample VMD session displaying myoglobin.
2. The Main window
3. The Main window animation controls
4. The Molecule File Browser window
5. The Display menu
6. Relationship between screen height, distance to origin, and the viewer
7. The Graphics window (in Draw Style mode)
8. The Graphics window (in Selections mode)
9. The Labels window
10. The Color window
11. The Material Window
12. The Render window
13. The Tool window
14. The Sequence window
15. The RamaPlot Window
16. Example showing red/green/blue gradients summed to produce the color scale.
17. The shift to the red component of the RGB scale caused by the value of ``min''.
18. RMS calculation and alignment extension
19. Graphical representation of a Colvars configuration.