David Hall wrote: > I'm trying run align2d on 3dxn chain a's pdb and it's sequence > provided by the pdb.
If I understand you correctly, you want to fill in the missing residues for a PDB file. The best way to do this is to create the alignment manually, using a text editor (although in principle you could write a script to parse the SEQRES and ATOM/HETATM records from the PDB file and use them to construct the alignment by comparison). This is the only real way to get the gaps where they are "supposed" to be. align2d will do a simple sequence-structure alignment, so it places the gaps wherever the dynamic programming decides is best. It does not know that one sequence happens to be the full PDB sequence and that it should therefore put the gaps where breaks in the PDB residue numbering occur.
Ben Webb, Modeller Caretaker