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

[Andreas Prlic]

Hi Raphael,

I don't think anything is wrong in particular. YG is a modified
nucleotide (Wybutosine, found at 3' to the anticodon, in eukaryotic
tRNA-PHE). At the present, the parser reads YG as a  group in the
atoms section, but does not understand what YG means if found in the
SEQRES. Is there anything you would like to be able to do with it?

Andreas




On Thu, Nov 6, 2008 at 8:24 AM, Raphael André Bauer
<raphael.andre.bauer at gmail.com> wrote:
> On Thu, Nov 6, 2008 at 5:20 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> 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:
> ... you are right. i was a bit too quick here.  one question still remains: do
> you know if the exception is "ok" in terms of the PDB file format or
> simply "wrong"
> because the exception thrown by the parser is wrong (or the parsing
> wents wrong?).
> if it is "wrong" i could easily fix it i guess.
>
> thanks for your help!
>
> raphael
>
>
>
>
>
>>
>> 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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>>
>