I see an example from the tutorial (Advanced Modeling, Modeling
ligands in the binding site) on an alignment similar to what I want.
However, I don't see the associated script to give this alignment
You make the alignment yourself, e.g. in a text editor. There is no
script to generate it for you automatically.
In this example, only the binding pocket of the 1emd structure was
included in the alignment. I would also need to know how not to
include a region in one of the other sequences.