I would like to post the code here but the data reading part is rather long. However I can post the dataprinting function where the problem may have occured? I use autoflush, yes I close my files. and the strange thing is this problem does not occur with some input and it occurs with others.. What I put below is only a short part of the program. Other relevant part could be the part where the pdb file is read from the given file but it seems like a writing buffer rather than reading buffer...

mainbody {

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

    #someother direct printings into file(direct meaning    printing i
+nto 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 w
+ant 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
}
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