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The alignment and superposition of protein structures are sometimes complicated by the presence of insertions or deletions in one structure or the other. The program ALIGN [Satow, Cohen, Padlan & Davies (1986). J. Mol. Biol.190, 593–604] was written to address this problem. The program provides information in its analysis of results to facilitate the understanding of transformations between structurally homologous subunits of protein structures.