This is the input:
>d1dlwa_ a.1.1.1 
slfeqlggqaavqavtaqfyangidmpnqtnktaaflcaalggpnawtgrnlkevhanmgvsnaqfttvighlrsaltgagvaaalveqtvavaetvrgdvvtvniqadatvatff
>d1uvyc1 b.1.1.1 
niqadatvatffngidmpnqtnktaaflcaalggpnawtgrnlkevhanmgvsnaqfttvighlrsaltgagvaaalveqtvavaetvrgdvvtvslfeqlggqaavqavtaqfya

##</code><code>##

My expected output (each in a .fa file):
>1dl_a_
slfeqlggqaavqavtaqfyangidmpnqtnktaaflcaalggpnawtgrnlkevhanmgvsnaqfttvighlrsaltgagvaaalveqtvavaetvrgdvvtvniqadatvatff
>1uvy_c1 
niqadatvatffngidmpnqtnktaaflcaalggpnawtgrnlkevhanmgvsnaqfttvighlrsaltgagvaaalveqtvavaetvrgdvvtvslfeqlggqaavqavtaqfya

##</code><code>##

#!/usr/bin/perl -w
@PDBchain;
@PDBcode;
@pdbString;
@SCOPclass;
$count =0; #SET A COUNTER FOR NUMBER OF ENTRIES

open (IN, "$ARGV[0]");
my @array;

while (<IN>)
{
        my $pdbId = $_;
	chomp($pdbId);
	push @array, $pdbId;
	print $pdbId;
	print "\n\n";
	if ($pdbId =~/>d(\d\w\w\w)(\w[_\d])\s(\w)/)
        {
                $pdbString[$count] = "";
                $PDBcode[$count]=$1; #SAVE PDB CODE
                print $PDBcode[$count];
                print "\n";
                $PDBchain[$count]=$2; #SAVE PDB CHAIN
                $SCOPclass[$count]=$3; #SAVE SCOP CLASS (A,B,C,D,E,F,G)
                $count++;
                next;
        }
        else
        {
                $pdbString[$count].=$pdbId;
        	next;
         }
        print $pdbString[$count]; #this prints the complete fasta sequence per entry!
        print "\n\n";
}
close IN;

print "Total number of entries: ".$count. "\n"; #COUNT TOTAL NUMBER OF PDBS REPRESENTED

for(my $i=0;$i<$count;$i++)
{
         open (OUT, ">>$PDBcode[$i]_$PDBchain[$i].fa");
         print OUT ">",$PDBcode[$i], "_", $PDBchain[$i], "\n";
         print OUT $pdbString[$i]; 
         #WHY AM I UNABLE TO PRINT THE SEQUENCE HERE?
         close OUT;
}