If your files contain multiple headers just flag it and get on with it.... If not just exit after the initial run of TITLE tokens runs out

my $header = 0;
my $title  = 0;
my $string = '';

while (<DATA>) {
    $header = 1 if /^HEADER/;
    $title  = 1 if /^TITLE/ and $header;
    if ( $header and $title ) {
        if ( /^TITLE\s+(.*)/ ) {
          $string .= $1;
        } else {
            $header = $title = 0;
            $string =~ s/\s+/ /g;
            print "$string\n";
            $string = '';
        }
    }
}    


__DATA__
HEADER    METAL BINDING PROTEIN                   31-AUG-98   1BSW    
+          
TITLE     ACUTOLYSIN A FROM SNAKE VENOM OF AGKISTRODON ACUTUS AT PH   
+          
TITLE    2 7.5                                                        
+          
COMPND    MOL_ID: 1;                                                  
+          
COMPND   2 MOLECULE: ACUTOLYSIN A; 
TITLE    NO 2 7.5  
TITLE    NO 2 7.5  

HEADER    METAL BINDING PROTEIN                   31-AUG-98   1BSW    
+          
TITLE     ACUTOLYSIN A FROM SNAKE VENOM OF AGKISTRODON ACUTUS AT PH   
+          
TITLE    1 2 3 4 5                                                    
+              
COMPND    MOL_ID: 1;                                                  
+          
COMPND   2 MOLECULE: ACUTOLYSIN A; 
TITLE    NO 2 7.5  
TITLE    NO 2 7.5
[download]

cheers

tachyon

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