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  1. or download this
    downloadFile.do?fileFormat=FASTA&compression=NO&structureId=2CU3
  2. or download this
    >2CU3:B|PDBID|CHAIN|SEQUENCE
MVWLNGEPRPLEGKTLKEVLEEMGVELKGVAVLLNEEAFLGLEVPDRPLRDGDVVEVVALMQGG
>2CU3:A|PDBID|CHAIN|SEQUENCE
MVWLNGEPRPLEGKTLKEVLEEMGVELKGVAVLLNEEAFLGLEVPDRPLRDGDVVEVVALMQGG
  3. or download this
       $filename =~ s[^.+/][];  # you have this one already
   $filename =~ tr/?&/_/;   # just add this one (turns all ? and & int
+o _)