[Biojava-l] Different chain lengths using struc.getChainByPDB and iterating over a structure and it's chain

[Raphael André Bauer]

Hey everybody,


suppose the following PDB file:
	
....
ATOM   2847  OD1 ASP A 370      14.470   9.116  16.553  1.00 57.47           O
ATOM   2848  OD2 ASP A 370      12.601   9.313  15.410  1.00 57.77           O
ATOM   2849  N   ASN A 371      17.114   9.968  15.979  1.00 46.04           N
ATOM   2850  CA  ASN A 371      18.177   9.691  16.946  1.00 46.67           C
ATOM   2851  C   ASN A 371      19.555  10.072  16.403  1.00 46.52           C
ATOM   2852  O   ASN A 371      19.848  11.250  16.177  1.00 43.37           O
ATOM   2853  CB  ASN A 371      18.174   8.209  17.345  1.00 49.12           C
ATOM   2854  CG  ASN A 371      16.969   7.829  18.189  1.00 52.62           C
ATOM   2855  OD1 ASN A 371      16.762   6.652  18.502  1.00 55.93           O
ATOM   2856  ND2 ASN A 371      16.168   8.824  18.568  1.00 52.06           N
TER    2857      ASN A 371
HETATM 2858 ZN    ZN A 400      43.465  12.734  15.463  1.00 24.94          ZN
HETATM 2859 ZN    ZN A 401      46.414  14.165  16.934  1.00 30.14          ZN
HETATM 2860  N9  ADE A1114      50.418   9.820  20.124  1.00 80.38           N
HETATM 2861  C8  ADE A1114      50.489  11.169  20.334  1.00 80.76           C
HETATM 2862  N7  ADE A1114      49.492  11.773  19.748  1.00 80.58           N
HETATM 2863  C5  ADE A1114      48.715  10.855  19.124  1.00 79.77           C
....


1) If I use

//struc being the parsed pdb file
returnChain = struc.getChainByPDB("A", 1);

I get chain A EXCEPT everything after the TER (ZN and ADE is excluded
in this example).

2) If I iterate over the complete file using something like

//struc being the parsed pdb file
int nrModels = struc.nrModels();
			
for (int modelNr = 0; modelNr < nrModels; modelNr++) {
List<Chain> chains = struc.getModel(modelNr);
int nrChains = chains.size();
for (int chainNr = 0; chainNr < nrChains; chainNr++) {

//this chain contains also the ZN and the ADE



So maybe I am getting something wrong here. Is this effect wanted by
the PDB parser?


Thanks!


Raphael