I'd use a hash of arrays (see perldsc - Perl Data Structures Cookbook). The chain will be the key, there will be two values in each array: the Z-coordinate and the position. Then just iterate the input and test whether the new line should go to the hash or not: 
my %hash;
while (<>) {
    my ($chain, $pos, $zcoor) = (split)[4, 5, 8];
    $hash{$chain} = [$pos, $zcoor]
        if not exists $hash{$chain} or $pos < $hash{$chain}[0];
}

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In reply to Re: How to select specific lines from a file by choroba
in thread How to select specific lines from a file by Anonymous Monk

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