Perl's Command Switches (perlrun) Can be a big help.

C:\Users\Bill\forums\monks>type aria.dat
ATOM 9 H5T THY C 1 107.274 35.359 -9.821 0.00 0.00 N1 H
ATOM 10 O5' THY C 1 107.686 36.230 -9.553 1.00 0.00 N1 O
ATOM 11 C5' THY C 1 108.813 35.973 -8.710 1.00 0.00 N1 C
ATOM 12 H5' THY C 1 109.513 35.493 -9.239 0.00 0.00 N1 H
ATOM 13 H5'' THY C 1 108.495 35.550 -7.861 0.00 0.00 N1 H
ATOM 14 N1 THY C 1 107.956 38.157 -5.232 1.00 0.00 N1 N
ATOM 15 C6 THY C 1 107.862 39.006 -4.149 1.00 0.00 N1 C
ATOM 16 H6 THY C 1 108.479 39.755 -3.910 0.00 0.00 N1 H
ATOM 17 C2 THY C 1 107.024 37.166 -5.449 1.00 0.00 N1 C
ATOM 18 O2 THY C 1 107.071 36.398 -6.397 1.00 0.00 N1 O
ATOM 19 N3 THY C 1 106.027 37.104 -4.506 1.00 0.00 N1 N

C:\Users\Bill\forums\monks>type aria.pl
#!perl -pibak
use feature 'state';
state $num = 0;
$num++;
s/^ATOM\s\d+/ATOM $num/;

C:\Users\Bill\forums\monks>perl aria.pl aria.dat

C:\Users\Bill\forums\monks>type aria.dat
ATOM 1 H5T THY C 1 107.274 35.359 -9.821 0.00 0.00 N1 H
ATOM 2 O5' THY C 1 107.686 36.230 -9.553 1.00 0.00 N1 O
ATOM 3 C5' THY C 1 108.813 35.973 -8.710 1.00 0.00 N1 C
ATOM 4 H5' THY C 1 109.513 35.493 -9.239 0.00 0.00 N1 H
ATOM 5 H5'' THY C 1 108.495 35.550 -7.861 0.00 0.00 N1 H
ATOM 6 N1 THY C 1 107.956 38.157 -5.232 1.00 0.00 N1 N
ATOM 7 C6 THY C 1 107.862 39.006 -4.149 1.00 0.00 N1 C
ATOM 8 H6 THY C 1 108.479 39.755 -3.910 0.00 0.00 N1 H
ATOM 9 C2 THY C 1 107.024 37.166 -5.449 1.00 0.00 N1 C
ATOM 10 O2 THY C 1 107.071 36.398 -6.397 1.00 0.00 N1 O
ATOM 11 N3 THY C 1 106.027 37.104 -4.506 1.00 0.00 N1 N

C:\Users\Bill\forums\monks>type aria.datbak
ATOM 9 H5T THY C 1 107.274 35.359 -9.821 0.00 0.00 N1 H
ATOM 10 O5' THY C 1 107.686 36.230 -9.553 1.00 0.00 N1 O
ATOM 11 C5' THY C 1 108.813 35.973 -8.710 1.00 0.00 N1 C
ATOM 12 H5' THY C 1 109.513 35.493 -9.239 0.00 0.00 N1 H
ATOM 13 H5'' THY C 1 108.495 35.550 -7.861 0.00 0.00 N1 H
ATOM 14 N1 THY C 1 107.956 38.157 -5.232 1.00 0.00 N1 N
ATOM 15 C6 THY C 1 107.862 39.006 -4.149 1.00 0.00 N1 C
ATOM 16 H6 THY C 1 108.479 39.755 -3.910 0.00 0.00 N1 H
ATOM 17 C2 THY C 1 107.024 37.166 -5.449 1.00 0.00 N1 C
ATOM 18 O2 THY C 1 107.071 36.398 -6.397 1.00 0.00 N1 O
ATOM 19 N3 THY C 1 106.027 37.104 -4.506 1.00 0.00 N1 N
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