yes, think your right i have replaced the column with white space that needs replacing: input file:

0.00  X  1.000  
0.530 X  0.753
# output values for residue    1
     0
# input   
0.00   X  1.00  
0.555  X  0.683
# output values for residue    2
     0
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so replace the X's with data from oter file:

0.99
0.99
0.99
0.99
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i thought something along the lines

open (FILE, "<filetoedit");
open (NEED, "<insert");
open (OUT, ">dine");

@array = <NEED>;
$end = scalar @array;

$count = 0;

while (<FILE>) {

for ($count = 0; $count < $end; $count++) {
###then some how replace x's with the new values
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