[Biojava-l] Chain order

[Enrico Morelli]

Dear,

I've to get data from PDBs to do some calculations. I wrote the following code to get atoms coordinate.

 for (Chain c : structure.getChains()) {
     for (Group g : c.getAtomGroups()) {
          for (Atom a : g.getAtoms()) {
		matnum = a.getPDBserial();
                matnam = a.getName();
                mrsnam = g.getPDBName();
                mchain = g.getChain().getName();
                mrsnum = g.getResidueNumber().getSeqNum();
                xmetal[0] = a.getX();
                xmetal[1] = a.getY();
                xmetal[2] = a.getZ();
            }
      }
}

But I noticed that the Chain loops over an alphabetical order of the chains not in the PDB order.

If in my pdb I've:

HETATM 4271 CU    CU C1139      -0.625  16.357 -12.867  1.00 50.00   CU
ATOM    729  NE2 HIS A  96       0.676  16.709 -11.347  1.00 40.00   N
ATOM   2863  NE2 HIS C  96       0.770  16.556 -14.258  1.00 40.00   N

My loop starts with the second atom, not the first. So my calculations doesn't work.

Is there a way to have the chains in the pdb order?

Thanks
-- 
-----------------------------------------------------------
  Enrico Morelli
  System Administrator | Programmer | Web Developer

  CERM - Polo Scientifico
  via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
------------------------------------------------------------