Not all of us can see in 3-D.

3d-glassesThis seems to be forgotten in every article I’ve seen on this so far.

For example, Jan Stokes writes “Eventually, though, you’ll take the 3D plunge–we all will, because we won’t have a choice.” [My emphasis added.]

Erm, no. Some of us don’t have a choice: we can’t.

Not unless they add some feature that reverts them to 2-D. (Who’d want that? It’d be cheaper to buy an “old style” TV.)

This was also a minor issue for me looking at the three dimensional structure of molecules displayed on the earlier molecular graphics displays (in the late 1980s and early 1990s).

My background is analysing the sequence, structure and function of the “macromolecules of life”: DNA, RNA and proteins. I am particularly interested in the latter, especially those that interact with DNA to control the use of genes.

Glutamine synthetase

Glutamine synthetase

Proteins have complex three-dimensional structures and are viewed using molecular graphics software like PyMol or Chimera (for what it’s worth I usually use Chimera).

Stereo display systems on computers are usually equipped with stereo glasses. These typically alternately allow one eye to see the image, then then the other by blocking each eye in turn by “flooding” the LCD-based (liquid crystal display) lens. This is synchronised to the graphics card, which projects left- and right- images with the proper timing for your left eye to see only the “left” image and vice versa for your right eye.

I’ll tell you about the early graphics molecular graphics systems I used some other time, but one problem you get seeing a complex 3-D image with only one eye and poor depth cuing is an inversion effect, where your brain inverts it’s perspective of the shading to effectively “invert” the image.

(I should emphasis that was the case on the old systems. Even then it was more of a minor annoyance than a real stumbling block. The depth perception in today’s graphics are so much better this isn’t an issue anymore.)

A simple fix to was to slightly rock the image, so that the foreground moves in front of and with a greater travelling distance that things further back.

It’s sometimes called “wiggle stereoscopy”.

A crude example of this is in the image to the right. This image moves too much and too fast for my liking, but it illustrates the principle of the idea. (My experience was that you only needed to occasionally move or “rock” objects slightly occasionally to “remind” yourself of the relationship of the shading, etc., to cue the depth perception, rather than the constant motion shown here.)

Modern molecular graphics programs offer a related effect as gentle “rocking” option. (It’s much more elegant that what is shown to your right.)

Similarly, animations of 3-D objects are helpful when giving talks for people unfamiliar with the shapes of the objects. Those studying them often forget it’s very hard to someone not familiar with a complex shape to quickly take it in presentations of it from new angles; it’s better to rotate to the new position if possible.

(I don’t expect to see this in movies anytime soon. I imagine audiences would be very queasy after watching a few minutes of Avatar rocking in front of their faces…)