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When aligning more than one structure, STAMP will usually create alignments that are fairly meaningless within regions that are not structurally equivalent across all structures. Such regions may have meaning for particular sub-families of structures, but for the purposes of display, are nonsensical. STAMP_CLEAN is a useful program that takes a STAMP alignment file and `cleans up' such gaps. To run the program, for example (using the POSTSTAMP output file generated above):

stamp_clean 3 > globin.5.clean

will create a file globin.5.clean where all gaps not lying within structurally equivalent regions, and having fewer than 3 aligned residues in a row (i.e blocks where all sequences are not aligned with gap) are shortened to their minimum length.