[Biojava-l] Question about StructureTools and PDBFileReader

[Martin Heusel]

Hi,

i read a PDB file with PDBFileReader.getStructure and want to extract
the backbone of a chain with StructureTools. Now i have seen that for
entries e.g.

ATOM   3505  N   GLN A  27      32.144  27.054   0.696  1.00 47.70           N
ATOM   3506  CA  GLN A  27      32.507  26.162  -0.401  1.00 42.73           C
ATOM   3507  C   GLN A  27      31.388  26.137  -1.437  1.00 40.44           C
ATOM   3508  O   GLN A  27      30.205  26.248  -1.096  1.00 41.47           O
ATOM   3509  CB  GLN A  27      32.729  24.738   0.121  1.00 42.51           C
ATOM   3510  CG  GLN A  27      34.124  24.449   0.611  1.00 39.02           C
ATOM   3511  CD  GLN A  27      34.158  23.301   1.593  1.00 41.90           C
ATOM   3512  OE1 GLN A  27      33.982  22.143   1.214  1.00 39.58           O
ATOM   3513  NE2 GLN A  27      34.386  23.615   2.869  1.00 43.85           N
ATOM   3514  N   SER A1027      31.762  25.988  -2.703  1.00 33.42           N
ATOM   3515  CA  SER A1027      30.776  25.929  -3.769  1.00 31.11           C
ATOM   3516  C   SER A1027      29.915  24.723  -3.462  1.00 27.99           C
ATOM   3517  O   SER A1027      30.418  23.706  -2.991  1.00 29.25           O
ATOM   3518  CB  SER A1027      31.449  25.746  -5.130  1.00 22.71           C
ATOM   3519  OG  SER A1027      30.542  25.185  -6.056  1.00 28.95           O
ATOM   3520  N   LEU A2027      28.619  24.838  -3.718  1.00 25.68           N
ATOM   3521  CA  LEU A2027      27.714  23.743  -3.444  1.00 23.42           C
ATOM   3522  C   LEU A2027      27.489  22.933  -4.694  1.00 24.27           C
ATOM   3523  O   LEU A2027      26.750  21.950  -4.675  1.00 28.95           O
ATOM   3524  CB  LEU A2027      26.391  24.278  -2.906  1.00 23.54           C
ATOM   3525  CG  LEU A2027      26.547  25.090  -1.619  1.00 22.93           C
ATOM   3526  CD1 LEU A2027      25.179  25.430  -1.056  1.00 26.74           C
ATOM   3527  CD2 LEU A2027      27.361  24.285  -0.603  1.00 19.54           C

the two residues SER and LEU are not counted. However, the fasta file
from pdb.org website shows both residues for that chain. I wonder how
the two entries A1027 and A2027 are interpreted by StructureTools.

Thanks for any hints

Martin