My template is a homodimer and I want to model my target also as a
hmodimer.
The sequence of the chain A of homodimer in the PDB file is like:
MKQA.............G.
The sequence of the chain B of homodimer in the PDB file is like:
MKQA.............GK.
If the sequences are different, then it isn't a homodimer...
But if
there is a slight difference in the two chains, like in this case the K
residue is extra, then what should I do?
Either model it as a heterodimer (in which case you wouldn't add the
Modeller symmetry restraints) or align that extra K residue with a gap
in your model sequence (or add a gap to the end of the template A chain
and align it with a K in your model sequence), so that the two chains
are identical in the model.