VMD User's Guide

Chapter 4User Interface ComponentsVMD provides several methods for the user to control and interact with the molecular display. Theprimary methods are by using the mouse, either in the graphics window or in the different graphicaluser interface (GUI) forms provided by the program. In addition to the mouse, VMD also supportsa number of more advanced input devices such as the Spaceball, Magellan, and Phantom, whichprovide the ability to manipulate molecules with six degrees of freedom. Some devices such as thePhantom can also provide haptic (sense of touch) force feedback. VMD also provides a text consoleinterface for executing built-in commands or running scripts. This chapter describes how to usethe mouse-based user interfaces, and some of the advanced input devices supported in VMD. Thethe text and scripting interface is described fully in chapter 8.4.1 Using the Mouse in the Graphics WindowThe graphics window is labeled VMD OpenGL Display and contains a view of the molecules andother objects which make up the scene. When the mouse is in the graphics display window, it maybe used to perform the following actions such as:• Rotate, translate, or scale the displayed molecules• Select, or ‘pick’ atoms or other objects in order to move them, or label them• Translate and rotate a set of atoms• Apply a force (acceleration) to a set of atoms• Move the lightsUser-defined keyboard accelerators, or hot keys, are also available when the mouse is in the graphicsdisplay window. These keys are bound to VMD text commands, which are executed when the keyis pressed. VMD has many built-in default hot key commands (see Tables 4.1, 4.2, 4.3 and 4.4).Users can add new hot keys, overriding default settings if desired.4.1.1 Mouse ModesThe mouse is in one of several modes at any time; the current mouse mode determines the effect ofpressing and releasing mouse buttons or the mouse wheel while the mouse is in the graphics window.23