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          );

  ## generate the alignment and echo it in the RasMol window
  my $alignment = $self->alignment();
  chomp($alignment);
  $alignment =~ s/^.*$/echo '$&'/gm;
  $stringio->print("echo 'Alignment:'\n",
           $alignment, "\n");

  ## color the identities, similarities, mismatches
  ## simultaneously selects/colors and echos the legend
  $stringio->print("load pdb inline\n",    # must load before selecting
           "echo \n",
           "echo 'Legend:'\n",
           "echo '  set names in quotes may be used with select'\n");
  my @select_me;
  if ( @select_me = $self->get_identities() ) {
    my @deco = ('cartoons','color blue');
    $stringio->print( $self->_format_select( @select_me ),
            "define identities selected\n",
            map { "$_\n" } 'wireframe off',@deco );