bestkarollo wrote: >> rdabrk__291E> Sequence difference between alignment and pdb : >> x (mismatch at alignment position 1) >> Alignment IQKVQDDTKT LIKTIVTRIN DI LDFI PGLHPILTLS KMDQTLAVYQ QIL >> PDB IQKVQDDTKTLIKTIVTRINDILDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRN >> Match * * * >> Alignment residue (UNK) does not match pdb residue I (ILE), >> for align code 1AX8 (atom file 1AX8), pdb residue number "3", chain " "
You need to remove the spaces from your alignment file, since Modeller considers ' ' to be a valid residue type. As you can see above, the alignment sequence has spaces in, but the PDB sequence does not.
Ben Webb, Modeller Caretaker