On Fri, Nov 7, 2008 at 8:26 AM, Andreas Prlic <[EMAIL PROTECTED]> 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 > <[EMAIL PROTECTED]> wrote: >> On Thu, Nov 6, 2008 at 5:20 PM, Andreas Prlic <[EMAIL PROTECTED]> 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 >>> <[EMAIL PROTECTED]> 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 >>>> _______________________________________________ >>>> Biojava-l mailing list - Biojava-l@lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>> >>> >> > _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l