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
.