I'm not the best when it comes to regex's, but I would use something like this:

    my $s = qq|%%Atom Coords
    -1.13 12.16 6.15
    %%End Frame|;

    $s =~ s/^%%Atom Coords\s*(.*)\s*%%End Frame$/$1/;   

    print $s;
[download]

May I also suggest (and I will suggest this to myself, too ;-)) that you pick up a good book on this subject.

- wil