Stereo Viewing "... the best introduction to
stereo viewing on the web ... "
(RasMol Home Page: What's
New? 97/09/14) Gale Rhodes rhodes@usm.maine.edu
Department of Chemistry University of Southern Maine
Viewing Stereo Pairs On Computers
Viewing Stereo Pairs In Journals and Textbooks
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 be a much more effective explorer of molecular structure if you learn to
see in 3D. Most structural biologists learn to view stereo views by two methods:
convergent and divergent viewing.
Viewing In 3D On A Computer Monitor Or Classroom
Screen
First turn on stereo viewing with your
molecular graphics program. For most graphics programs, set the stereo viewing angle to -5
degrees (that's minus five). RasMol is backwards; for convergent viewing, set the
angle to 5 degrees with the command stereo 5 (this is the default in RasMol).
Or work with this convergent stereo pair of the heme (space filling) and
histidine ligands (ball and stick) in cytochrome b5*:
How To Do It
To view most computer and projected
stereo images, you need to look at the left-hand image with your right eye, and at the
right-hand image with your left eye (called convergent or cross-eye viewing). Here's how
to develop the skill at your computer.
Gaze at the stereo pair, 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. 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.
Viewing Stereo Pairs In Texts And Journals
These instructions are for a printed
stereo pair, which you can find in some biochemistry textbooks or in journal articles (try
a recent issue of Science -- look for an article announcing a new protein structure
determination).
If you have no printed pairs, print this page with a color printer, and use
this divergent version of the previous stereo pair*:
If you can't print the image, use it on the screen, or use your molecular
graphics program to make a satisfactory image. First, turn on stereo viewing. Shrink the
graphics window so that the stereo pair is small -- about the same size as a stereo pair
in a textbook. The distance between image centers must be no more than the distance
between your eyes, 6 to 7 cm (for those still in the Dark Ages, that's about 2 & 1/2
inches). For divergent viewing in most graphics programs, set the stereo angle to 5
degrees (that's plus five -- this is often the default setting). RasMol is
backwards; for divergent viewing, set the RasMol stereo angle to -5 degrees (thats minus
five) with the command stereo -5.
How To Do It
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). Here are two methods to try.
Put your nose on the page between the two views. With both eyes open, you
will see the two images superimposed, but out of focus, because they are too close to your
eyes. Slowly move the paper away from your face, trying to keep the images superimposed
until you can focus on them. (Keep the line between image centers parallel to the line
between your eyes.) When you can focus, you will see three images. The middle one should
exhibit convincing depth. Try to ignore the flat images on either side.
Another method -- the one I used when stereo pairs first appeared in the
biochemical literature (can anyone tell me where?): Photocopy a stereo pair from a text or
journal article, and cut off the copied page above the pair, leaving the pair at the very
top of the page. Then hold the page just below eye level, and look out above it at a
distant object. You will notice below your line of sight that the two views are blurred,
but superimposed on each other, because your eyes are looking more or less parallel to
each other to the distant object. Now move the picture upward into your line of sight,
trying to keep the images superimposed, and try to focus on them. As with the first
method, you will see three images -- the middle one is three-dimensional.
Here's another technique, suggested by Nicolas Guex.
Tape a divergent stereo pair to a mirror, just below eye level. Then look at
your eyes in the mirror above the image. Slowly bend your knees so that your view passes
through the stereo pair on the way to looking at your eyes below the image, and then
slowly rise again and repeat. At some point, as you cross the pair, the images should
fuse, and you should find it easy to focus on the three-dimensional image, because your
point of focus for looking at your reflection is not far off.
(In trying for divergent viewing, you may stumble into convergent viewing;
after all, it's actually a more natural thing for your eyes to do. With the image above,
if you mistakenly view it cross-eyed instead of wall-eyed, it will appear very strange
because the depth cues of the image (light, shadow, and hidden surfaces) conflict with
those provided by the double image. In addition, the space-filling heme atoms will appear
to be inside out, or concave rather than convex. Finally, the histidines (ball and stick)
will appear closer to you than the front edge of the heme, while they are actually near
the middle of the heme.)
Practice, Practice, Practice
Viewing either convergently or divergently becomes easier
with practice. Once your mind sees a pair as a single 3D image, it recalls the experience,
and resists your efforts less with each try. I can automatically snap a stereo pair --
convergent or divergent -- into superimposition, and I no longer think about exactly what
I am doing. Suddenly, there is a vivid, three-dimensional object floating above the screen
or page. I've been doing it since 1969 (that's a hint about the source of the first
biochemical stereos!), and I've suffered no damage to my vision. It's very handy to be
able to use the stereo pairs in Science and other journals without digging up a
viewer. Such important tasks as interpreting electron-density maps from x-ray
crystallography are practically impossible without this skill.
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Stereo images prepared with SwissPdbViewer.