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Core Text Commands

 

Most of VMD was originally written without the Tcl interface. The text interpreter used (which is still available as a compile time option) treated the commands in a slightly different form than Tcl does. Because we did not rewrite the old commands when Tcl ws added, there is a slight difference in usage between the old style interface (the ``core'' commands) and the new Tcl functions. For the most part, these are subtle and not important. For more information see the section on "writing scripts" (???)

  
Table 11.1: Summary of core text commands in VMD .

All text commands in VMD are composed of one or more words or phrases separated by white space, and terminated by a newline. Since the parser now uses Tcl, a ``phrase'' is text surrounded by double quotes or by a matching set of open and close braces. (Please read the Tcl manual to better understand what constitutes the end of a statement.) The first word of each command indicates the general purpose for the command, and the following words specify the exact type of command to execute. Table 11.1 summarizes the text commands in VMD by listing the first words, and describing the general purpose for commands starting with those words. Since VMD can be compiled with optionally included components and features, commands labelled optional may not be available in your version of VMD .

The commands described in the following sections are listed by name, and followed by a list of the available arguments. If an argument is optional, it is enclosed in []s. If only one of a list of arguments is needed, the list is enclosed in <>s and the items are seperated by |. Words in italics indicate a string or value to be specified by the user.

 

animate

These commands control the animation of a molecular trajectory and is used to read and write animation frames to/from a file. Play/Pause/Rewind a molecular trajectory.

 

axes

The axes (orthogonal vectors pointing along the x, t, and z directions) can be placed in any of 5 locations on the screen, or turned off. Does any place list where to change the axes colors???

 

color

Change the color assigned to molecules, or edit the color scale. All color values are in the range 0 ... 1. Please see the section on colors for a full description of the various options. ???

 

debug

Turn on/off printing of debugging messages. This will have no effect if VMD was compiled without the debugging option (the standard distribution was not compiled with debugging).

 

display

Change various aspects of the graphical display window. For information about the options, see the section describing the display form. ???

 

echo

Turn on/off echoing of text commands to the console. When this is turned on, text commands read from a file or from the VMD prompt are echoed to the screen before they are executed. Do not confuse this with the standard unix echo command.

 

exit

Quit VMD.

 

external

(Tcl) Communicate Tcl commands between different processes based on the Tcl-DP RPC functions (optional). This command can set the machine up as a server (listening for commands) or client (sending commands) or both.

 

help

Display the on-line help file with an HTML viewer. Typing `?' will also bring up the help file. See ??? for information on how to change the default viewer (which is Mosaic). This command uses the index of the VMD User's Guide to determine the appropriate URL for the help request. Since you may prefer to use a local site for help information, see ??? to find out how to get the HTML distribution of this guide and how to modify VMD to use it.

 

journal

Same as log.

 

label

Turn on or off labels for the four categories: atoms, bonds, angles, or dihedral angles. Once a label is created (given the list of associated atoms) it can be turned on or off until it is deleted. The value of the label over the trajectory can be saved to a file and viewed with an external program.

 

light

There are four light sources, numbered 0 to 3, used to illuminate graphical objects. They are point sources located at infinity so the only controls are to rotate a light or turn it on or off. A dotted line from the light to the axis can be turned to help show where the light is located.

log

   Turn on/off logging a VMD session to a log file. This will create a log file with commands for all the actions taken during the session. The log file may be played back later by using the `play' command or the Tcl `source' command. The only actions recorded are those which change the state of the VMD \ display, so straight Tcl commands are not saved. All of the core VMD commands will write to the log. ??? Check the 'external' command

To write log information to the file `off', use the file name `./off'.

 

menu

The menu forms of the GUI Control or query the on-screen GUI menu forms.

list forms namds???

 

mol

Load, modify, or delete a molecule in VMD. In the following, molecule_number is a string describing which molecules are to be affected by the command. Is is of the form <m1|m2|...|mN>, where mN is one of the following: all, top, active, inactive, displayed, on, off, fixed, free, or one of the unique integer ID codes assigned to the molecules when they are loaded.

 

molecule

Same as mol.

 

mouse

Change the current state (mode) of the mouse.

 

play

Start executing text commands from a specified file, instead of from the console. When the end of file is reached, VMD will resume reading commands from the previous source. This command may be nested, so commands being read from one file can include commands to read other files.

 

quit

Same as exit.

 

remote

Set up VMD to connect to or start a remote simulation program (optional).

 

render

Output the currently displayed image (scene) to a file.

 

rock

Rotate the current scene continually at a specified rate.

 

rot

Rotate the current scene around a given axis by a certain angle.

 

rotate

Same as rot.

 

rotation

Same as rot.

 

run

Same as play.

 

scale

Scale the current scene up or down.

 

sim

Control the state of a remote simulation after it is connected (optional).

 

simulation

Same as sim.

 

stage

Position a checkerboard stage on the screen.

 

stop

Same as exit.

 

tracker

Initialize and control external spatial tracking devices.

 

trans

Translate the objects in the current scene.

 

translate

Same as trans.

 

user

Add user-customized commands to the graphics display popup menu.

 

vmdlog

 

(Tcl) By default this procedure does not exist. If it is created, (nearly) every command that affects the display state of VMD is passed to it as its single parameter. This can be used as an alternative interface to the log command.

 

vmdinfo

(Tcl) Returns information about this version of VMD .

This function is available without Tcl and the information is displayed to the screen.

 

wait

Specify a number of seconds to wait before reading another command.



next up previous contents index
Next: Vectors and Matricies Up: Text User Interface Previous: Tcl



Andrew Dalke
Tue May 14 16:49:45 CDT 1996