To Make a Menu Appear: There are at least two ways to do this. One method is to click in the GL Display window with the rightmost mouse button. A popup menu will appear. While holding down on the right mouse button, drag down to the "Show Form" option. A list of check boxes will appear, allowing you to activate a number of common menus. A second way to access this menu list is through VMD's main form. This main form is probably on your screen already (look for the bank of radio buttons with the blue "VMD" at the top). If it is not, you can make it visible via the "Show Form" option described above.
To Make a Menu Disappear: Just click on the blue-lettered bar at the top of the menu.
To Load a Molecule (i.e. bR): Activate the Mol menu as described above. Click on the button labeled "Load From Files." This will bring up another form from which you can specify the type of the file to load. By default VMD expects a PSF structure file and a coordinate set in PDB format. But for our purposes, a PDB file alone will do. Click on the "pdb only" option in the blue browser list. Notice that the pink text entry blanks change to reflect the new file type. Click on the "Select pdb" button next to this pink text box. The FileSelector menu which appears will allow you to specify the directory in which VMD is to search for the data file. First type /nfs/cairo/workshop for the directory and then choose segbR.pdb in the browser list which appears. Click "Ready" and then click "Load Molecule" in the files menu to finish loading the protein bacteriorhodopsin (bR).
To Scale, Rotate, or Translate: There are three basic mouse modes in VMD: Scaling, Rotating, and Translating. To switch amongst them, simply hit 'r', 's', or 't' on the keyboard while the mouse is in the GL Display. Experiment with these modes and note how the cursor changes to indicate the current operation. For rotations, the left mouse button controls rotation about axes parallel to the screen while the right mouse button controls rotation about the axis perpendicular to the screen. In translation mode, the left mouse button controls translation parallel to the screen, while the middle button controls translation in and out of the screen. Finally, in scaling mode, both the left and middle buttons control global scaling when the mouse is moved left or right, but the middle button causes larger changes.
To Change Drawing Methods: If necessary, activate the Graphics menu as described above. Click on the drop down menu next to the words "Drawing Method." Choose your desired representation.
To Change Coloring Methods: If necessary, activate the Graphics menu as described above. Click on the drop down menu next to the words "Coloring Method." Choose your desired coloring scheme.