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  VMD supports selection based on the one-letter amino acid sequence with the sequence selection keyword. This allows selections of the form

	sequence APD
	sequence "C..C"       (might be used to pick out zinc fingers)
	sequence AATCGGAT

Unlike the other string selection commands which take one of three types of strings, all the strings for sequence are taken as regular expressions (though strings with non-alphanumerics must still be quoted to get past the input parser). The method works by taking each of the protein and nucleic acid fragments (pfrag and nfrag) in turn and constructing the one-letter amino acid sequence. If a regular expression matches any of the sequence, the atoms in the matching residues are selected. Multiple matches are allowed, though they cannot overlap. As is usual with regular expressions, the largest possible match is made, so take care with expressions like C.*C.

Justin Gullingsrud
Tue Apr 6 09:22:39 CDT 1999