Three-dimensional models have performed a pivotal role in the development of molecular biology since its origins in the 1950s, both as an experimental technique and in raising public awareness and political and financial support for the discipline. Perhaps the best-known molecular model is Watson and Crick's double helix in the photographs by Antony C. Barrington-Brown. The procedure adopted by Watson and Crick (1953) was to build a model which could be checked against the experimental data and refined to produce the 'best-fit', a common technique among crystallographers of the time (de Chadarevian, 2002). The importance of model-making was reflected in a Medical Research Council Laboratory of Molecular Biology gallery at the Science Museum in London, 'Living molecules', which ran for 12 years from 1987. In January 2003 an exhibition of molecular models, including a replica of Watson and Crick's original construction, opened in Cambridge to celebrate the Golden Jubilee of the Double Helix.

The first models of biomolecules were fashioned from plasticine and sticks, but by the late 1950s purpose-made construction kits had been devised and were available commercially to scientists world-wide. Great difficulty remained however, in representing large, complex three-dimensional molecular structures on paper. As Lawrence Bragg remarked in 1967 about John Kendrew's work on the 3-D structure of myoglobin:

"It is extraordinary that ... [Kendrew] got his Nobel Prize in effect for unpublished work."

(quoted in de Chadarevian, p. 146)

Several solutions to this problem were attempted. First photographs of physical models, then artists' representations of them were tried. These drawings, often completed with painstaking care over many months, tried to show the structures accurately yet reveal hidden detail that could not be seen in photographs of solid objects.

For a period, perhaps reflecting the popularity of 3-D movies in the 1950s, 3-D anaglyph images of molecules became common and entire books of these pictures were published (see, for example, Phillips and North, 1973). Anaglyphs are pairs of red and green (or red and blue) images that require glasses with correspondingly-tinted lenses to see the 3-D effect. These images are produced as though seen from the same distance from the model, but using two viewpoints about 5 cm apart (similar to the distance between the eyes). The two coloured images are superimposed when printed. Filters in the glasses allow only one image to enter each eye, and the viewer's brain combines the pictures to create an impression of depth. Red/green images are often used in the UK while red/blue images are popular in the USA.

In the 1980s physical models were replaced in research laboratories by computer-generated images. Although stereo pairs of full-colour images remain popular, some viewers find these hard to see (the observer usually has to go 'cross-eyed'). Alternative methods require the use of expensive polarising filters or LCD-shuttered spectacles. The following method combines the accuracy of computer modelling with the ease of viewing anaglyph images.

This article appeared in the March 2003 issue of the School Science Review.

ANAGLYPH IMAGES FROM
MOLECULAR MODELLING SOFTWARE

It is relatively simple to create 3-D images from molecular model data and apart from the tinted glasses this requires no camera or special equipment. Molecular modelling software such as RASMOL is available free-of-charge and is well-known in schools (Millar, 1996).

Creating the image pair
Although RASMOL can automatically create stereo pairs for viewing by the 'cross-eyed' method, such pictures cannot be combined to make anaglyph images. Instead, the two images have to be created 'manually'. This is done as follows.

First, open a molecular structure (.pdb) file using RASMOL and rotate and re-size the image (using the 'ZOOM' command) until you have the view you desire. From the screen-top menu, choose the type of image projection you require (e.g., 'sticks' or 'cartoon'). Switch the colour of the image to 'monochrome' and change the background colour of the image to white [Command: BACKGROUND WHITE]. Selecting options such as 'shadow' and 'specular' may help to define the image more clearly. Export the image e.g., as a JPEG or TIFF file, giving it a suitable name such as 'Image1.jpg'. Next, rotate the molecular model in the y axis by -1.5-2 ° [Command: ROTATE Y -2]. A little experimentation will allow you to find the optimum amount of rotation required for a given model and viewing distance. Export this second image with a suitable name e.g., 'Image2.jpg'. Hint: if you are preparing several pairs of images in one session, it may help to use names for partnered images that are obviously linked such as 'Wallace' and 'Gromit' or 'Watson' and 'Crick'.

Combining the images
Once a pair of images has been created, additional software is needed to combine them and add the colour necessary for the 3-D effect. Although image manipulation software such as Adobe PhotoShop can be used to create anaglyphs, numerous stand-alone packages for creating stereo images are available free-of-charge or as shareware. The Web site Stereoscopy.com maintains a useful list on its 'downloads' page. The two images produced by RASMOL are simply imported by the programme and an anaglyph image can be output.

With a little patience, series of anaglyph images may be combined to create dramatic 3-D animations.

REFERENCES

Watson, J.D. and Crick, F.H.C. (1953) Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid Nature 171, 737-738. This is available on-line from: http://www.nature.com/genomics/human/watson-crick

de Chadarevian, S. (2002) Designs for Life. Molecular biology after World War II. Cambridge; Cambridge University Press.

Phillips, D.C. and North, A.C.T. (1973) Protein structure. Oxford; Oxford University Press.

Millar, N. (1996) Computer modelling of biological molecules: free resources on the internet. School Science Review 78 (282) 55-60.

ACKNOWLEDGEMENTS

Images for the 3-D anaglyph image of DNA on the cover of the March 2003 issue of the School Science Review were produced using RASMOL, written by Roger Sayle in 1995. This molecular modelling software is available free-of-charge from the Web site listed below.

Data for the B-form of DNA was supplied by the Protein Data Bank (PDB code: 1D66) using co-ordinates adapted from Marmorstein, R. et al (1992) DNA recognition by GAL4: Structure of a protein-DNA complex. Nature 356, 408.

WEB SITES

Making 3-D anaglyphs
http://graphicssoft.about.com/library/weekly/aa082499.htm

Stereoscopy.com
http://www.stereoscopy.com

The Stereoscopic Society
http://www.stereoscopicsociety.org.uk

RASMOL
http://www.umass.edu/microbio/rasmol

Protein Data Bank
http://www.rcsb.org/pdb

Nucleic Acid Database
http://ndbserver.rutgers.edu/NDB/ndb.html

SOURCES OF 3-D GLASSES

You can make your own 3-D glasses by drawing a template with red and green lenses, then printing it on acetate (overhead projector) film. Alternatively, there are numerous suppliers of 3-D glasses. In the UK, a wide variety is available from:

3-D Images Ltd, 31 The Chine, London, N21 2EA.
T: + 44 (0) 20 8364 0022/0104
F: + 44 (0) 20 8364 1828
W: http://www.3-dimages.com

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