$k=0;	
open (IN, '6U9D.pdb.txt');
%amino_acid_conversion = (ALA=>'A',TYR=>'Y',MET=>'M',LEU=>'L',CYS=>'C',GLY=>'G', ARG=>'R',ASN=>'N',ASP=>'D',GLN=>'Q',GLU=>'E',HIS=>'H',TRP=>'W',LYS=>'K',PHE=>'F',PRO=>'P',SER=>'S',THR=>'T',ILE=>'I',VAL=>'V');
while (<IN>) {
	if ($_=~m/HEADER\s+(.*)/){
	print ">$1\n"; }
	if ($_=~m/^SEQRES\s+\d+\s+\w+\s+\d+\s+(.*)/){
		$seq.=$1;
	$seq=~s/ //g;}
}

#THIS IS THE PART I CANT SEEM TO FIGURE OUT
for ($i=0;$i<=length $seq; $i+=3) {
print "$amino_acid_conversion{substr($seq,$i,3)}"; #All seems well with the sequence I get the desired output
$k++;}
print "\n";
if ($_=~m/^ATOM\s+\d+\s+\w+\s+\w+\s+\w+\d+\s+(\S+)\s+(\S+)\s+(\S+)/){   #the parentheses are the xyz coordinates respectively
	$x+=$1;
	$y+=$2;
	$z+=$3;
}
		

$xgk=($x/$k); $ygk=($y/$k); $zgk=($z/$k); 
print "$xgk $ygk $zgk \n";