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

[Andreas Prlic]

Hi Raphael,

The parsing is perhaps a bit verbose and might be misleading in this
case.  It does not break or stop after printing this exception. If you
investigate the loaded structure object in the end you can see that
the toString() looks like this:

structure  4TNA IdCode: 4TNA Classification: AMINO-ACID TRANSPORT
DepDate: Wed Apr 12 00:00:00 PST 1978 Technique: X-RAY DIFFRACTION
Resolution: 2.5 ModDate: Tue Apr 01 00:00:00 PST 2003 Title: FURTHER
REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE
 chains:
chain 0: >A< TRNAPHE
 length SEQRES: 0 length ATOM: 76 aminos: 0 hetatms: 14 nucleotides: 62
chain 1: > <
 length SEQRES: 0 length ATOM: 4 aminos: 0 hetatms: 4 nucleotides: 0

Andreas

On Thu, Nov 6, 2008 at 2:07 AM, Raphael André Bauer
<raphael.andre.bauer at gmail.com> wrote:
> 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
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