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

[Raphael André Bauer]

On Fri, Nov 7, 2008 at 8:26 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> 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?
I think how it is handled now is ok for me (just a short notice about
the unknown YG).

Thanks!

Raphael

>
> 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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>>>>
>>>
>>
>