Stereo Vision

Introduction

Being able to visualize and experience strucutre in 3-D is an essential skill, if you are at all serious about understanding the molecules of molecular biology. This is not sufficiently realized in the field: many molecular biologists in the field have never invested the effort it takes to learn the skill and thus get by regardless. The catch is: unless you have experienced and worked with stereo images, there is no way of understand how much you are actually missing. But once you have used the skill, you'll regret not having been taught earlier. Seing molecules in 3-D is like the difference between seing a photograph of a place and actually being there. In 3-D you can apreciate size, scale, distance, spatial relations all at a single glance. I would claim: you can't understand structure unless you experience it in 3D.

From 2D to 3D
Images we see on screen or on paper are two-dimensional projections f three-dimensional objects.

Even though hardware devices exist that help in the three-dimensional perception of computer graphics images, for the serious structural biologist there is really no alternative to being able to fuse stereo pair images by looking at them. VMD is an excellent tool to practice stereo vision and develop the skill. Stereo images consist of a left-eye and a right-eye view of the same object, with a slight rotation around the vertical axis (about 5 degrees). Your brain can accurately calculate depth from these two images, if they are presented to the right and left eye separately. This means you need to look at the two images and then fuse them into a single image - this happens when the left eye looks directly at the left image and the right eye at the right image.

Some people find convergent (cross-eyed) stereo viewing easier to learn. I recommend the divergent (wall-eyed) viewing - not only because it is much more comfortable in my experience, but also because it is the default way in which stereo images in books and manuscripts are presented. The method explained below will only work for learning to view divergent stero pairs.

Physiology

In order to visually fuse stereo image pairs, you need to override a vision reflex that couples divergence and focussing, this is something that needs to be practiced for a while. Usually 5 to 10 minutes of practice twice daily for a week should be quite sufficient. It is not as hard as learning to ride a bicycle, but you need to practice regularily for some time, maybe 10 or 20 sessions of 3 to 5 minute over a period of a week or two. Once you have acquired the skill, it is really very comfortable and can be done effortlessly and for extended periods. You will enter a new world of molecular wonders !

Instructions

Here are step by step instructions of how to practice stereo-viewing with VMD.

• Load a small protein into VMD (1UBQ will work just fine) and display this as a simple backbone model.
  • VMD Main → Representations → Drawing Method: Tube
  • Increase the tube radius to 1.0; choose coloring by Index.

A simple molecular model
For instructions to generate this scene, see above.

• Set the stereo display to SideBySide:
  • VMD Main → Display → Stereo → SideBySide

SideBySide stereo view
For instructions to generate this scene, see above.

• Resize the window, until two equivalent points on the protein are the same distance on the screen as the pupils of your eyes are apart (this is usually about 6 cm). Don't just guess, measure the distance, and adjust your on-screen scene to better than two or three millimetres of the correct separation.

SideBySide stereo view
For instructions to generate this scene, see above.

• Touch your nose to the screen and look right at the two images. Make sure you see the right image with your right eye, the left with your left eye. Of course, since you are so close, the images will be blurred and out of focus. Nevertheless, you should see one solid, three dimensional shape in the centre, two peripheral images of the same on the sides. Actually you see three copies of the same scene, but only the fused, centre scene appears three-dimensional; the other two become less noticeable as you practice more, your brain simply begins editing them out. Slowly rotating the protein with the mouse helps generate the impression of a 3-D object floating before you. (With VMD you can use the mouse to give the molecule a slow spin and it will continue to rotate).

• Once you see the object in 3-D, try to move your head backwards slowly, until the structure comes into focus by itself. Do not voluntarily try to focus, since this will induce your eyes to converge and you will lose the 3-D effect. After a short while, you will probably lose the 3-D effect. Once you lose the 3-D effect, pause, look somewhere else and start over.

• Practice this patiently, two times daily for some 3 to 5 minutes. Stop, when your head feels funny. Don't force yourself.

It should take you about a week to master this, with regular training it will become very easy. And, the best thing is, you do not easily forget this skill. It is like riding a bicycle, equalizing pressure in your eustachian tubes while scuba diving, or circular breathing to play the didgeridoo: once you teach your body what to do, it remembers. And it expands your horizon.

Examples

Below, there is a script to set up a stereo-view of 2IMM. Simply copy the script from the textarea and paste it into the VMD command line window. The commands get executed line by line and it is easy to change parameters and arguments and see what effect this has.

Trouble shooting

[TBC]

Resources and References

• Stereopsis - Wikipedia article on why we see in three dimesions
• Stereoscopy - Wikipedia article on the techniques for stereo images