Click on the graphics window to make it active. Notice the row of buttons across the top of the window. Click the first one on the left. You see the same window dialog (Window Attributes) that comes up when you start the program. Notice the features of the display that you can adjust with this window. One is the window size, but there is an easier way to adjust the size of the graphics window. Click Cancel on this dialog, and then move the cursor, which at the moment has a curved arrow on it, to the bottom right corner of the graphics window. When you are in the right position, the cursor changes to an arrow (standard pointer). Now you can click and drag the lower right corner of the window to change its size. Adjust the size to suit you. Do not hide the Control Panel, and leave at least an inch at the bottom of the screen for later use of the Align window.
The next three buttons control movement of the model. From left to right, they translate, zoom, and rotate. Try each one: first click to activate the button, then drag the mouse left and right to see the effects. Notice that the cursor changes to show you which button is selected. Watch the cursor as you press the tab key repeatedly. Pressing tab cycles through the three movement functions from left to right. Now hold down the shift key while pressing tab repeatedly. This action cycles through the movement functions from right to left. If you keep your left hand at the keyboard while using the mouse, you can select any movement function in a single operation, without having to point and click on the buttons.
Spend some time manipulating the model to get used to the controls. Then press the help key in the cluster of keys between the keyboard and the numeric keypad, or the = key on the top of the numeric keypad (right mouse button on PC). Either of these keys centers the model and adjusts its size to fit the screen, without rotating. This is a very handy feature. Whenever the view becomes awkward, just press either of these keys to give a convenient view of the model. (When this tutorial mentions the = key, it always means the = key of the numeric keypad, not the one on the main keyboard.)
Because SPdbV displays only in wireframe, without depth cueing, stereo viewing will help you to carry out mouse functions precisely. Here's some instruction in Stereo Viewing.
Display: Stereo View
<help>
SPdbV displays a stereo pair. Press help to
adjust size and centering. You may need to adjust stereo settings
further in order to achieve comfortable viewing. Use the Window
Attributes dialog again (first button on the left at the top of the
graphics window) to set stereo view rotation and separation. Try a
rotation of -4 degrees (that's minus four) for cross-eyed
viewing. Decrease the separation if the views are too far apart to
fit the window (first you must click to turn off Adjust Stereo
Separation). Each time you change the separation, close the
dialog and press help to adjust the model and see how well it
fits the window. For any functions that require clicking on an atom
while viewing in stereo, you must click on the atom in the left
image. The right image does not respond to mouse clicks. You can
carry out the remainder of the tutorial in stereo, if you wish. You
can turn stereo on and off by holding down the command key and
pressing t (remember sTereo) on the
keyboard.
Here's another handy manipulation feature: option-click (PC: right-mouse click) the name of a residue in the Control Panel. SPdbV selects the residue and centers the view on its alpha carbon (CA). Zoom in very close to the model, so that the centered residue fills the screen. Option-clicking a residue in the Control Panel is very useful for jumping to a specific residue in your model.
Take time to PLAY with the tools introduced in this section.
For more information about manipulating models, click on SPdbV User Guide in the Contents frame (at left), and read the section entitled Move and Rotate.