VMD User's Guide
VMD User's Guide
VMD User's Guide
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8.2 Tcl/TkThe standard distribution is compiled with Tcl, which add a complete scripting language includingvariables, loops, and conditionals along with a standard method for communicating with otherprograms via standard TCP/IP sockets. Versions 1.2 and later also include the Tk toolkit, forcreating menus with buttons bound to one’s favorite actions.Tcl (short for Tool Command Language, developed by John Ousterhout) is an embeddable andextensible scripting language. In other words, Tcl sits inside <strong>VMD</strong> as a language interpreter whereit can execute its standard language commands or the various <strong>VMD</strong> specific extensions.<strong>VMD</strong> uses Tcl and Tk version 8.4.1. We refer you to http://www.tcl.tk/ for more informationabout Tcl.8.3 Tcl Text CommandsAll Tcl commands in <strong>VMD</strong> are composed of one or more words or phrases separated by whitespace, and terminated by a newline. In Tcl, a “phrase” is text surrounded by double quotes or bya matching set of open and close braces. The first word of each command indicates the generalpurpose for the command, and the following words specify the exact type of command to execute.Table 8.1 summarizes the text commands in <strong>VMD</strong> by listing the first words, and describing thegeneral purpose for commands starting with those words.The commands described in the following sections are listed by name, and followed by a list ofthe available arguments. If an argument is optional, it is enclosed in []s. If only one of a list ofargumentsisneeded,thelistisenclosedins and the items are separated by |. Words in italicsindicate a string or value to be specified by the user.8.3.1 animateThese commands control the animation of a molecular trajectory and are used to read and writeanimation frames to/from a file or Play/Pause/Rewind a molecular trajectory.• dup [ frame frame number ] molId: Duplicate the given frame (default “now”) of moleculemolId and add the new frame to this molecule.• forward: Play animation forward.• for: Same as forward.• reverse: Play animation backward.• rev: Same as reverse.• pause: Pause animation.• prev: Gotopreviousframe.• next: Gotonextframe.• skip n: Setstrideton+1 frames.• delete all: Delete all frames from memory.90