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 globin.5.post 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.