try{ PDBFileReader read=new PDBFileReader(); Structure pdb=read.getStructure(filename); System.out.println("PDB code :"+pdb.getPDBCode()); List chains=Collections.synchronizedList(new ArrayList()); chains=pdb.getChains(); for(Iterator iter=chains.iterator();iter.hasNext();){ Chain c=(Chain)(iter.next()); System.out.println("Chain :"+c.getName()+"\n"+"Seq aa :"+c.getAtomSequence()); for(int j=0;j<c.getAtomLength();j++){ for (int k=0; k < c.getAtomGroup(j).size(); k++ ){ Atom a=c.getAtomGroup(j).getAtom(k); System.out.println("Name : "+a.getName()+" X : "+a.getX()+" Y : "+a.getY()+" Z : "+a.getZ()); } }