[Biojava-l] Question about StructureTools and PDBFileReader

[Martin Heusel]

Hi Andreas,

thanks for your fast help. Sorry it was my fault, i was irritated by a
SCOP sequence:

>d1a4ka1 b.1.1.1 (A:1-112) Immunoglobulin light chain kappa variable
domain, VL-kappa {Mouse (Mus musculus), cluster 1.1}
ELVMTQTPLSLPVSLGDQASISCRSSQSLLHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQVTHVPPTFGGGTKLEIKRTVAA

it says chain A sequence numbers 1-112 but the sequence is 117 long.
At sequence number 27 there is

ATOM   3506  CA  GLN A  27      32.507  26.162  -0.401  1.00 42.73           C

and five additional residues afterwards (only CA)

ATOM   3515  CA  SER A1027      30.776  25.929  -3.769  1.00 31.11           C
ATOM   3521  CA  LEU A2027      27.714  23.743  -3.444  1.00 23.42           C
ATOM   3529  CA  LEU A3027      28.008  22.622  -7.045  1.00 26.03           C
ATOM   3537  CA  HIS A4027      28.614  18.875  -6.927  1.00 27.10           C
ATOM   3547  CA  SER A5027      31.052  17.066  -9.205  1.00 31.92           C

so there is a sequence number 27 and five additional numbers 1027 - 5027

Then it goes further with 28

ATOM   3553  CA  ASN A  28      27.957  15.242 -10.411  1.00 26.69           C

So if i iterate over a CA Atom array from 1 to 28 in this case, i
correctly get the first 28 CAs.  So my assumption that i don't get
these additional CAs was not correct, i missed the last five. I'm
sorry i should have debugged more closely.

My question is now if it's possible to get the CAs or groups in a
sequence number interval?

Also i wonder what these additional groups between 27 and 28 are.

best regards

  Martin