The problem is not over when we have collected our X-ray pictures. A lot of computation is still required to produce the "electron density". This is a blurry image of where the atoms are inside our protein. From sequencing the gene encoding the protein, we know what order to expect for the different amino acids. We now have to interpret our blurry image in terms of this sequence. This is normally done by eye using powerful 3D graphics computers.

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We build up the protein in stages. First of all we try to see the overall fold of the protein, tracing the path taken by the backbone. Then we add the side-chains, which are the unique parts of each amino acid. The movie below shows this schematically. The grey lines surround regions of high electron density, which should be where the atoms go. The result is an atomic structure, which can be used to increase our understanding, or to help produce medicines, or simply to look at.

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