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 <[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 - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
