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CHAINSAW is a model editing program for use in molecular replacement. Given a sequence alignment between template and target, it modifies the template structure on a residue-by-residue basis by pruning nonconserved residues while leaving conserved residues unchanged. Three degrees of pruning are possible. An internal alignment algorithm is used to cope with any residues that may be missing from the X-ray structure. CHAINSAW has been successfully used as a tool to assist in solving a number of protein structures.
Norman Stein (Tue,) studied this question.