mainbody {

    my $index=0;
    my $input=$mw->getOpenFile();
		
    open FILE, ">$input" or die $!;
    FILE->autoflush(1);

    #someother direct printings into file(direct meaning    printing into file within this body without calling other functions as below)

    tie @lines, 'Tie::File', $input or die $!;
    #somemore direct printings into file

    #below are functions that get arrays, some indices and prints them into file

                 
    if($pdb_active)
         {
         printtoDataBase(\@exp_beta_alpha,16,6); #below
         printtoDataBase(\@exp_beta_heavy,32,6);
         }
     
    #other printing functions	

    untie @lines;
    close FILE;

  }

sub printtoDataBase #the part where the problem occurs
	{
	my ($dataArray,$column,$ref_size)=@_;
			
	my $index=0;
	$repeat=10;
			
	my @dataArray=@$dataArray; #deref
			
	for (;$repeat<($residuenumber+10); $repeat++)
		{
		my $size = length $dataArray[$index];
		if($size>($ref_size))
                   {
                   $size=($ref_size);
                   }	
					#refsize tells up to how many digits do the user want the number to be displayed
				                                     
        substr($lines[$repeat],($column),($size))=
        substr($dataArray[$index],0,($size));
				
        $index++;
	
        } # above function gets the b-factor numbers in the file found the stated part by the substr
}