Jump Over Left Menu
Spots before the Eyes
The Atlas Microdensitometer in Use
The measurement of photographic intensities usually involves weeks of tedious visual estimation but a microdensitometer - a machine recently installed at the Atlas Computer Laboratory - will do the job in a day. This machine will provide a service for the many groups throughout the country using X-ray crystal structure techniques to determine molecular structure.
The technique of X-ray crystallography involves exposing a suitable crystal to a narrow beam of X-rays. The wavelength of the X-radiation is around 0.1 nanometers which is very close to the spacing between adjacent atoms in the molecules of which the crystal is composed. This means a diffraction effect occurs-the beam of X-rays interacts with the electrons in the crystal and a number of diffracted beams result, emerging from the crystal at various angles. The intensities of the various diffracted beams vary widely and depend upon the distribution of electrons in the crystal. If the crystallographer can measure these intensities then it is possible to work backwards, using rather complicated mathematical techniques, to derive the positions of the electrons, and hence the atoms, in the crystal. Such results are quite accurate - the distances between atoms in a molecule may be calculated to within a few parts in ten thousand and molecular geometries can be accurately determined. Within the limitations imposed by the need for a crystalline sample the technique is of general application. Simple structures such as diamond have been studied in great detail and workers have recently determined the structures of biologically significant molecules such as RNA and haemoglobin, with thousands of atoms to one molecule.
The Atlas microdensitometer will play its part in the collection of the data needed for a crystal structure analysis. In a typical experiment a crystal is mounted at the centre of a cylindrical cassette containing a pack of 3-5 pieces of X-ray film. The crystal is rotated in a beam of X-rays and the resulting diffracted beams are recorded as small black spots on the films when they are developed. A set of ten film packs, each containing 200-1,000 spots, makes up the initial data for the crystal structure determination. After digitization it is necessary to estimate the relative intensity (blackness) of each spot.
It used to be a crystallographer's nightmare estimating these intensities by visual comparison with a set of calibrated intensities. Now it can be done automatically with the aid of the computer controlled microdensitometer. Each film is mounted on the drum of the machine and the drum then rotates at 4 revolutions per second. During each revolution an optical system measures the intensity of the light transmitted through the film at points every 0.1 mm around the drum. After each revolution the optical system is moved at 0.1 mm intervals along the axis of the drum and in this way the whole film is covered in the steps of 0.1 mm in each direction.
The measured intensity values are passed to a computer, which has sufficient time between reading to compute the intensities of all the spots on the film, despite the fact that readings are taken at the rate of 14,000 per second. The use of a pack of films in the cassette enables a greater intensity range to be covered than would be possible with one film, since intensities fall off by a factor of about 3 when the diffracted Xrays pass through each piece of film.
The machine requires one operator and can process a pack of films in an hour, extracting up to a thousand spot intensities. The complete data for a crystal structure can thus be collected in a day. The accuracy is limited by the experimental conditions and the quality of the films, rather than by the machine, which should certainly be sufficient for the average structure determination.
The microdensitometer is not of course limited to processing X-ray films although it will spend most of its time doing so. There are a wide number of applications which require accurate density measurements from photographic films on transparencies. For example, the machine has occasionally been used to digitize X-rays of miners' lungs for pneumoconiosis studies, or photographs of handwriting for optical character recognition work.
Michael Elder is a senior scientific officer in the Applications Software Group at the Atlas Compute Laboratory.