Labels Form

Figure 4.8: The Labels form

This form is used to manipulate the labels which may be placed on atoms, and the geometry monitors which may be placed between atoms. Labels are selected with the mouse. Once selected, the Labels form can be used to turn different labels on or off or to delete them entirely. Also, labels displaying geometrical data such as bond lengths may be graphically displayed using this form.

Label categories

The Category chooser (in the upper left) is used to select which category of labels to manipulate. The different label categories include:

• Atoms, which are shown as a text string next to the atom listing the name and residue of the atom;
• Bonds, which are shown as dotted lines between the atoms with the bond length displayed at the bond midpoint;
• Angles, which are shown as dotted lines between the three atoms with the angle displayed at the center of the defined triangle;
• Dihedrals, which are shown as dotted lines between the four atoms with the dihedral angle (the angle between the planes formed by the first three atoms and the last three atoms) shown at the midpoint of the torsional bond.
• dihedrals

All the labels for the selected category which have been previously added are displayed in the browser in the center of the form. The line itself contains from 1 to 4 atom names, depending on the category; the atom names have the form

<residue name><residue id>:<atom name>

followed by either (on) or (off). The last word indicates if the label is turned on or off.

Modifying or deleting a label

A label can be turned on or off without deleting it, by selecting the label in the central browser and pressing the Hide button. To turn it back on, select it again then press the Show button. Press the Delete button to delete it. This browser allows multiple selections, which, for example, allows you to delete several labels at once. To select everything in the current category, press Select All; to unselect them, press Unselect All. If nothing is selected, the action is applied to everything. Thus, one way to turn everything off is to press Unselect All then press Hide. (It may seem counterintuitive, but it was done this way so all the labels could be deleted by just pressing Delete.)

Plotting a label's value

If the label has a numeric value (such as a bond length geometry monitor), it is easy to graph the change of the value over time (for multiple frames in an animation). The Graph button creates a temporary file for use by a graphing program, then optionally starts such a program to display the data. Each line of the file contains the frame number (starting at zero and expressed as a floating point number) followed by the value of the label for that frame.

Once the file is created, the text in Graph Command is executed to plot the data. By default, the text is xmgr %s, where the %s is automatically replaced with the appropriate temporary file name. When the graphing program finishes, the temporary file is deleted.

The default setup causes VMD to freeze until the graphing program finishes. It is possible to get around this by including an & at the end of the graph command, as in:

        xmgr %s &

This may sometimes cause a problem because VMD might delete the file before the program finishes reading it. If this is a problem, try:

        csh -c "xmgr %s &; sleep 4"

to cause VMD to wait a few seconds before deleting the file. You may have to increase the delay depending on the file size and type of program used. You may also try variations on the theme; for instance

        csh -c "xterm -e vi %s ; sleep 4"

will bring up a vi window with the data file.