[Biojava-l] YG and parsing error of PDB file

[Raphael André Bauer]

hi biojava-l,


i am getting the following exception:

badly formatted line ... SEQRES   3 A   76    C   C   A   G   A OMC U
OMG   A   A  YG   A PSU
org.biojava.bio.structure.io.PDBParseException: amino acid name is not
of length 3! (YG)


when i am trying to parse the pdb entry 4TNA [1] (a RNA structure). It
seems that YG [2] is an ordinary compound that is built into the RNA chain.


is this really an error inside the PDB file, or is this something
where the biojava parser confuses amino acids and hetero ids because of
their lengths? is there an approved biojava way where i can catch the
exception without breaking the rest of the parsing?


many thanks,

raphael

[1] http://bioinf-services.charite.de/supersite/resultHET.faces?hetid=YG
[2] http://bioinf-services.charite.de/supersite/resultPDB.faces?pdbid=4TNA