If I for instance wanted model myoogxyglobin based on hemoglobin which
is polydimer. In my example I used chain A for my modeling how do I
indicate for modeller to use just one ligand from the chain A.
In your alignment you have two sequences: the template and the model.
The ligand you want to model needs to be in both sequences, of course,
since Modeller builds the model sequence, and it needs to see the ligand
in the template in order to know what the model ligand should look like.
But your template sequence should contain *all* of the ligands that are
in the template PDB file. Just align the model ligand with whichever one
of the template ligands you want to use.
For example, if your template PDB contains 4 HETATM residues after the
amino acid chain, and you want to use only the second of these in your
model, your alignment should look something like
Alternatively, you can change the residue range in the template header
(structureX line) to instruct Modeller to stop reading the PDB once it
reaches a given ligand's residue number - then you don't need to list
all the ligands in the sequence, just those up to that residue number.
Or you can make a copy of the PDB file, and edit it in a text editor so
that it only contains the ligands you're interested in.