Most of us have come across 3D movies, like the recently released Ice Age 3D, which give a very real depth to image and videos as if they are not ON some screen but rather hanging in the air, thus truly making them 3 dimensional. This was achieved, in olden times, by using the green and red filters on spatially apart cameras and merging them via colored goggles. Now a days more sophisticated techniques of polarized light using polar filters is used which gives better resolution.
Here I am giving a method which enables a user to achieve that kind of depth without any fancy goggles or image, in fact I'll be using a normal PDB file and SPDBV as visualizing tool, you can use whichever tool you like.
Please follow the steps:
1) Obtain any suitable PDB file:
For this, Google the RCSB site, in the search bar type your favorite protein name, I am using myoglobin (though it is not my favorite). U can get the myoglobin pdb file here.
2) Open this pdb file in any suitable viewer, I am using SPDBV.
In SPDBV you will get 'Stereo' view in the 'Display' tab in the menu bar at the top or else press Ctrl + T to toggle stereo view.
Important note: The viewer MUST have the option of displaying in Stereo view.
3) Display this file in the Ribbon view.
For this go to 'Window' tab in menu bar and select on 'Control Panel' or else press Alt + , . Now right click on any of the "v"s in the 'show' & 'side' columns and right click in the empty 'ribn' column. This will replace the early model by a ribbon model.
4) Colour the ribbon structure suitably.
For this go to the 'Colour' tab in menu bar, go to 'act on.... ->' and select 'Ribbon'. Now again go to 'Color' tab in menu bar and select 'Secondary Structure Succession'.
Note: If your structure is in mesh form then you can 'Render in Solid 3D' by going to the 'Display' tab.
Now you should be looking at something which looks like the screen-capture below:
Here comes the hard part:
What I want you to achieve is a third image, in sharp focus, which has popped out of the screen and is hanging in the air about half way between your eyes and the monitor.
For this:
Sit about 1&1/2 to 2 feet from the monitor screen. Concentrate on the monitor screen, and move your eyeballs towards each other by trying to look at the point in between your eyes.
When you do this the 2 images on the screen merge to form a third image, stop!! and try to focus on the third image (if you keep going the three images will further separate into 4 image!!)
Now, first thing is getting the third image in between the 2 original image.
Second thing is focusing on this third image. For this move the protein molecule, a moving third image will help you get a sharp focus on it.
Once you have got the middle image into focus, you can see that it has become absolutely 3 dimensional and now no longer sits on the monitor but has popped out and is hanging in the air. Rotating the molecule you can actually see that the alpha helices are on top or behind those in the front.
Have Fun!!!
Why does this happen??
Well the effect is the simple stereoscopic effect which is more commonly encountered in sounds. Often when we are listening to MP3s using ear phones, sounds seem to travel from one ear into another essentially meaning the source is moving.
In case of vision also it works in a similar way. We have two eyes separated by some distance. Whenever we focus on an image, we actually see 2 different images by each of the eyes, these are super imposed on top of each other by our brain to form the one clear image. We also perceive depth because of this.
When we view the PDB file in stereo in the visualizer, it shows two seemingly identical images, but look closer, they are actually slightly different.
When you merge the two images and try to focus, the brain does the rest of the work and renders the image 3 dimensional.
2 comments:
Intriguing, and interesting as a post. However, what you describe in the last part of the post, is pretty much what happens with those goggles! The red transparent film would filter one part and a dissimilar part by the blue film. Eventually doing exactly what you are describing. So those 3D films you see, they are actually 2 pictures, where each is filtered through one eye. :) No strain on the eye huh!
Actually that is not all... Apart from the red and blue filters one more thing happens. When shooting the movie, 2 cameras are used. They are separated by a distance of around 2.5 inches, one with a red filter and other with blue filter. Thus the images that the 2 cameras capture are not identical, they have a kind of parallax. This is essential for the brain to perceive that 3rd dimension. Later the films from 2 camera are merged during editing. Thus what I am saying is, the filters aren't as important as having the parallax between the 2 images.
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