sub blast_filets {

  my ($PF_READ, $PF_WRITE);
  my $pid = open2($PF_READ, $PF_WRITE, $PROFIT)
    or die "Couldn't open pipe to profit. $!";

  my $filets1 = $_[0];
  my $filets2 = $_[1];
  my $range1 = $_[2];
  my $range2 = $_[3] || $range1;

  my @rmsd = ();
  my $count = 0;

  if ( @$range1 != @$range2 ) { 
    die "Ranges do not have equivalent zone sizes.";
  }

  foreach my $f1 ( @$filets1 ) { 
    print "REFERENCE $f1\n" if $VERBOSE >= 3;
    print $PF_WRITE "REFERENCE $f1\n";
    foreach my $f2 ( @$filets2 ) { 

      if ( $VERBOSE >= 3 ) { 
        print "MOBILE $f2\n";
        print "ZONE CLEAR\n";
        print "ATOMS CA\n";
        foreach my $i ( 0..$#$range1 ) { 
          print "ZONE $range1->[$i][0]-$range1->[$i][1]"
                  . ":$range2->[$i][0]-$range2->[$i][1]\n";
        }
        print "FIT\n";
      }
      print $PF_WRITE "MOBILE $f2\n";
      print $PF_WRITE "ZONE CLEAR\n";
      print $PF_WRITE "ATOMS CA\n";
      foreach my $i ( 0..$#$range1 ) { 
        print $PF_WRITE "ZONE $range1->[$i][0]-$range1->[$i][1]"
                          . ":$range2->[$i][0]-$range2->[$i][1]\n";
      }
      print $PF_WRITE "FIT\n";
      print $PF_WRITE "\n\n\n\n\n\n\n\n\n\n";

    }
  }
  print $PF_WRITE "QUIT\n";

  my $result ;
  #print "Reading results\n";
  while ( defined ($result = readline($PF_READ))) { 
       #print "RESULT = $result\n" if $VERBOSE >= 2;
       if ($result =~ /RMS: ([\d\.]+)/m) { 
         #print "Rmsd = $1\n";
          push @rmsd, $1;
          $count++;
       }  elsif ( $result =~ /Error/i ) { 
         print "Error: $result\n";
       }
  }
  
  my $result_wait = waitpid($pid, 0);
  if ( $result_wait != $pid ) { 
    die "Waitpid returned $result_wait instead of $pid. $?.";
  }

  #print "DONE WITH RMSD\n";
  my ( $rmsd, $stddev ) = Utility::Mean_and_Stddev (@rmsd);
  return ($rmsd, $stddev, $count, \@rmsd);
}