Free What Mad Pursuit by Francis Crick Page B

He boldly assumed that one could approximate the shape by an ellipsoid—a particularly simple type of distorted sphere. Then he looked at what little was known of the crystals of hemoglobin of other species of animal, on the assumption that all types of hemoglobin molecules were likely to have about the same shape. Moreover, he was not disturbed if the data did not exactly fit his model, since it was unlikely that the molecule was exactly an ellipsoid. In other words he made bold, simplifying assumptions; looked at as wide a range of data as possible; and was critical but not pernickety, as I had been, about the fit between his model and experimental facts. He arrived at a shape that we now know is not a bad approximation to the molecule’s real shape, and he and Perutz published a paper on it. The result was not of first-class importance, if only because the method was indirect and needed confirmation by more direct methods, but it was a revelation to me as to how to do scientific research and, more important, how not to do it.
    As I learned more about the main problem, I began to worry about how it might be solved. As I have said, the X-ray data contained just half the necessary information, though it was known that some of what was available was probably redundant. Was there any systematic way to use the available data? It turned out there was. Some years earlier a crystallographer, Lindo Patterson, had shown that experimental data could be used to construct a special density map, now called a Patterson. [All the amplitudes of the Fourier components are squared and all the phases are put to zero.]
    What did this density map mean? Patterson showed that it represented all the possible interpeak distances in the real electron density map, all superimposed, so that if the real density map frequently had high density a distance of 10 Å apart in a certain direction, then there would be a peak at 10 Å from the origin in the appropriate direction in the Patterson map. (One Ångstrom unit is equal to one ten-billionth of a meter.) In mathematical terms, this would be a three-dimensional map of the autocorrelation function of the electron density. For a unit cell with very few atoms in it, and using high-resolution X-ray data, one could sometimes unscramble this map of all the possible interatomic distances and obtain the real map of the atomic arrangements. Alas, for protein there were far too many atoms and the resolution was too poor, so that doing this was quite hopeless. Nevertheless, strong features in the Patterson could hint at broad features in the atomic arrangements, and indeed Perutz had predicted that the protein was folded to give rods of electron density, lying in a particular direction, because he saw rods of high density in that direction in the Patterson. As it turned out the latter rods were not really as high as he had imagined (he had at that time only the relative intensity of his X-ray spots, not their absolute value) so the folding was not quite as simple as he had conjectured.
    This calculation of the Patterson of his crystals of horse hemoglobin was a difficult and laborious piece of work, since in those days the methods, both for collecting X-ray data and for calculating Fourier Transforms, were, by modern standards, primitive in the extreme. Many crystals had to be mounted (since each would only take a certain dose of X rays before deteriorating); many X-ray photos had to be taken, cross-calibrated, measured by eye, and systematic corrections made. The calculations were not done on what we would now call a computer (that came later) but using an IBM punched card machine. They took an assistant three months and were very laborious. Then all the numbers obtained had to be plotted and contours drawn, till eventually one ended up with a stack of transparent sheets, each having a section of the Patterson density shown on them as contours. As I recall, the negative contours (the average correlation was taken