I use multiple sequence and one template pdb to get an improved
alignment. I also just use part of the protein around the active domain.
Should I also add the ... at all the other seqeunce as well as the one I
am modelling.
Modeller can use multiple templates (structures) to model a single
sequence (model) but not the other way round. Its alignment methods
don't work with ligands anyway, so for alignments you should turn
env.io.hetatm off and not use any '.' one-letter codes. Then add in '.'
where necessary for the modeling step.
Is there anything in particular I should keep in mine when
using acetyl-coA when it is an ligand.
No, Modeller doesn't care about the type of the ligand, so you don't
have to do anything special.