Using the scritp model-ligand.py I introduced a ligand in my model,
but the waters were no added. Did I omitted anything in the
alignment?
env.io.hetatm=True only tells Modeller to read non-water HETATM
residues. To read water as well, set env.io.water=True too.
Once you do this, you will also need to change your alignment, adding a
'w' residue to the template sequence for every water in the PDB.
Can I copy the waters coordinates from de template file to the
modelled one
Sure - if you want waters in your model too, add a 'w' residue in your
alignment to the model sequence, aligned to the water you want to copy
in the template sequence.
It is rare to actually include waters in comparative models, as they
generally don't add any useful information. If you have crystallographic
waters, however, it may be useful to include them, although you may need
to construct sensible restraints to your protein.
Ben Webb, Modeller Caretaker
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