VMD User's Guide

First Wordanimateatomselectaxescolorcolorinfodisplayexit, quitgettimestephelpimdlabellightlogfilematerialmeasuremenumolecule or molmolinfomouseplayrenderrockrotatescalestagetooltranslateuservmdinfovolmapwaitsleepDescriptionPlay/Pause/Rewind a molecular trajectory.Create atom selection objects for analysis.Position a set of XYZ axes on the screen.Change the color assigned to molecules, or edit the colormap.(Tcl) Obtain color properties for various objectsChange various aspects of the graphical display window.Quit VMD.Retrieve a timestep as a binary Tcl array (use for plugins)Display an on-line help file with an HTML viewer.Control the connection to a remote simulation.Turn on/off labels for atoms, bonds, angles, dihedral angles, or springs.Control the light sources used to illuminate graphical objects.Turn on/off logging a VMD session to a file or the console.Create new material definitions and modify their settings.Measure properties of moleculear structures.Control or query the on-screen GUI menu forms.Load, modify, or delete a molecule.Get information about a molecule or loaded file.Change the current state (mode) of the mouse.Start executing text commands from a specified file.Output the currently displayed image (scene) to a file.Rotate the current scene continually at a specified rate.Rotate the current scene around a given axis by a certain angle.Scale the current scene up or down.Position a checkerboard stage on the screen.Initialize and control external spatial tracking devices.Translate the objects in the current scene.Add new keyboard commands.(Tcl) Get information about this version of VMDCreate volumetric data based on molecular informationWait a number of seconds before reading another command. Animation continues.Sleep a number of seconds before reading another command. Animation is frozen.Table 8.1: Summary of core text commands in VMD.120