## 3. Manipulating the Model

Click on the graphics window to make it active. Notice the row of buttons in the Tool Bar above the window. Click the first one on the left. This is the Zoom/Center button. It automatically zooms to fill the screen with whatever is currently on display.

Prefs: Display
DeepView shows you the current attributes of the graphics window. Notice the features of the display that you can adjust with this window. One is the window size (measured in screen pixels), which gives you a precise way to set window size when making an image for printing. But there is an easier way to arrive at a convenient size for the graphics window, especially for arranging it among the other windows. 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 graphics window for later use of the Align window.

The next three buttons on the Tool Bar control movement of the model. From left to right, they translate, zoom, and rotate. Try each one: first left-click to activate the button, then left-click-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.

Linux: These buttons currently do not appear to be functional in DeepView 3.5.. However, identical functionality may be obtained, provided one is using a three-button mouse with the X display. The first, second and third mouse buttons provide rotation, translation and zoom respectively. In other words, pan the mouse with the respective mouse button depressed to rotate, translate or zoom into and out of, any figure.

Shifting among the three movement functions is even easier if you have a two-button mouse. Left-click drag gives you rotation, right-click drag gives translation, and left-plus-right-click drag gives zoom. In whatever way to zoom, you will find it more natural to zoom in by moving the mouse toward you, and zoom out by moving it away. It's as if you pull the model toward you or push it away with the mouse.

Technical Note on Zooming: This manner of "zooming" does not really change the position of the model in the imaginary three-dimensional space of the graphics window. Zooming "in" actually corresponds to narrowing the viewing angle, so that a smaller angle of your view fills the screen (as if you are moving closer to the model rather than pulling the model towards you). This may seem like a matter of semantics, but as you will see later, there is a way to actually move the model in the imaginary space (change its 3-dimensional coordinates), and this allows you to move one model with respect to others.

Spend some time manipulating the model to get used to the controls. Then press the = key (Mac) or <insert> (Windows or Linux). This action has the same effect as the Zoom/Center button on the Tool Bar. It fills the view with, and puts the center of rotation in the middle of, whatever is currently on display, whether it is one residue or the whole model. This is a very handy feature. Whenever the view becomes awkward, or if you suddenly lose the model, use the Center/Zoom function to give a convenient view of the model.

Because DeepView 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
DeepView displays a stereo pair.

Zoom/Center (using Zoom/Center button, or the appropriate key for your computer)
You may need to adjust stereo settings further in order to achieve comfortable viewing, as follows:

Prefs: Stereo Display
Use this dialog to set stereo view rotation and separation.

Technical Note on Stereo Rotation: One view of a stereo pair is produced by copying the other view, rotating the copy a few degress about the y (vertical) axis, and placing the two views side by side. To see in stereo, you need to look at one view with one eye, and the other view with the other eye. This duplicates what happens when you look at real objects. When you look at a scene, one eye sees a view that is slightly rotated with respect to what the other eye sees. From the disparity between what the two eyes see, you perceive differences in distance to various objects in the scene.

Try setting a rotation of -4 degrees (that's minus four) for cross-eyed viewing (see Stereo Viewing). Decrease the separation if the views are too far apart to fit the window or for comfort (for cross-eyed viewing, I use a separation of 180 pixels on a 17-inch laptop with 1140 x 900 screen). Each time you change the separation, close the dialog and Zoom/Center 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 (alt on Windows, I think) and pressing t (remember sTereo) on the keyboard.

Linux: Use Alt-T. Windows:

Here's another handy manipulation feature: option-click (Windows: right-mouse click) the name of a residue in the Control Panel. DeepView 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.

Linux: This functionality currently seems to be missing. Also, there doesn't seem to be a clear-cut mapping between the 'option' key on the Mac and a corresponding one on the Linux keyboard.

### Review

- For easy manipulation of the model with a two-button mouse, it's left-click drag to rotate, right-click drag to translate, and both-click drag to zoom.
- For a one-button mouse, switch among rotation, translation, and zoom by pressing tab, or by choosing the appropriate button on the Tool Bar (buttons 2, 3, and 4 from the left).
- Zoom/center the model using = (Mac) or insert (Windows), or by clicking the zoom/center button (left-most button on Tool Bar.
- Center on a specific group by option-clicking the group name in the Control Panel.
- NEW TIP: Move the rotation center to the next residue by pressing a cursor button. Left cursor moves toward N-terminus, right cursor toward C-terminus. Try it.
- There are many ways to use the keyboard to modify the effects of DeepView commands. See Actions of Key Modifers.

Take time to PLAY with the tools introduced in this section.

For more information about manipulating models, click on DeepView User Guide in the Contents frame (at left), and read the section entitled Move and Rotate.

Next Section: 4. Selecting and Displaying

To The Molecular Level