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
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