(If you are resuming the tutorial after a break, start your desktop copy of RasMol, arrange the windows as in section 1, and open 3b5c.pdb. Restrict the view to residues 64-72, mainchain only. Turn on hydrogen bonds.)
Options: Stereo
RasMol displays the model as a stereo pair. Viewed
properly, a stereo pair gives you a three-dimensional (3D) image of
the model. Take time now to begin learning this skill. It takes some
practice, and you may find it slightly uncomfortable at first, but it
will become easy and comfortable, and your effort will be richly
rewarded by increased power to see spatial relationships and
structural details that are much harder to see any other
way.
Until you have seen molecular images in 3D, you cannot imagine how much you are missing, and how much easier it is to see structural details in stereo.
Here's how to view in 3D. Gaze at the screen, keeping your head level (don't tilt it left or right), and cross your eyes slightly. As you know, crossing your eyes makes you see double, so you will see four images. (By the way, you can't hurt your eyes or eye muscles by crossing your eyes, and you can't get them stuck that way.) Try to cross your eyes slowly, so that the two images in the center come together. When they converge or fuse, you will see them as a single 3D image. The fused image will appear to lie between two flat images, which you should ignore. When you are viewing correctly, you see three images instead of four. The center image is three-dimensional. At first, the 3D image may be blurred. Keep trying to hold the stereo pair together while you focus. The longer you can hold it, the more time your eyes have to adjust their focus. Usually, even before you begin to get the hang of focusing, the two central images lock together, because your mind begins to interpret them as a single 3D object.
Having trouble? Here's another approach. With your head level and about 2.5 feet from the screen, hold up a finger, with its tip about 6 inches in front of your face, and centered between the stereo pair on the screen. Focus on your finger tip. Without focusing on the screen, notice how many images you see there (they will be blurred). If you see four images, move your finger slowly toward or away from you eyes, keeping focused on your finger tip, until the middle pair of images converge. With your finger still in place, partly covering the converged pair, change your focus to the screen. The image partly hidden by your finger should appear three-dimensional. Your finger should still appear single, but blurred. With some practice, you can remove your finger and still keep the screen images converged into a stereo image.
Too often, people try only briefly and halfheartedly to view in stereo, and never try again. Almost anyone can view in stereo with a little effort and practice. The only ones who simply cannot are those who have acute amblyopia (one very weak eye). And those who say they can see just as much without stereo simply cannot imagine what they are missing. You can continue this tutorial with or without stereo viewing, but if you ever need to explore macromolecules on your own, you can be a much more effective explorer if you learn to see in 3D.
(This viewing method is different from that needed for viewing printed stereo pairs in textbooks and journals. To view most printed images, you need to view the left image with the left eye, and the right image with the right eye (called "divergent" or "wall-eye" viewing). In addition, with printed views, the distance between the images must be less than the distance between your eyes, so the images must be small. Viewers are available to magnify the image and to guide your eyes. To view larger stereo pairs, such as those on a computer or projection screen, you must use the method described above, and cross your eyes slightly to look at the right-hand image with your left eye, and at the left-hand image with your right eye (called "convergent" or "cross-eye" viewing). For most people, convergent viewing is easier to learn, but most structural biologists learn to view both ways without viewers. For more help, see Stereo Viewing.)
One unfortunate quirk of the current version of RasMol is that picking is sometimes unpredictable in stereo. You should always pick on the left image, but if you do not get proper response to picking, turn off stereo for picking by selecting Options: Stereo. (The check mark appears by the word Stereo when the stereo display function is turned on, and disappears when it is turned off -- this type of on/off command is sometimes called a "toggle".)