you can simply try to edit the PDB file manually using the something like

ATOM natom ZN ZN nres x y z

Since one of your templates (3GTT) contains Zinc ions (see HETATM record), your model should have contained the ions. I assume that you have tried to generate the model using the script model-default.py. The model-default.py is the most basic script modeller provides, therefore you can build over this script to modify it to your needs.

However, your problem should not be that complicated. Zinc in 3GTT acts as a ligand (coordination acceptor) to the structure. Therefore, I advise you to try model-ligand.py script that comes with Modeller package.

Now, as I explained above model-default.py can be modified very easily taking reference from the model-ligand.py and model-multichain.py.

Step 2:

1. Take the inspiration from file, wherein a Ligand is denoted by '.'

2. Add these dots '.' to align-multiple.ali file after the sequence of 3GTT and after your query.

3. You will  have your Apo form modelled with Zinc metal ion, in runtime.

Caution: I would advice against the addition of metal ion after the model is generated because, the Potential score you used to select your model will not be the same with the metal ion and therefore you may find it difficult to justify.

Cheers.:)

-Tjr

you can perform alignment followed by superimposition of your model with 3GTT via MatchMaker tool of chimera. After superimposition, just delete the protein chain of 3GTT keeping the HETATM coordinates (Zn2+).

just through pymol is the easiest way

You can use model-ligand.py and you should also set env.io.hetatm to True, then This is done by using the (’.’) residue type in your alignment (both in the template(s) and the model sequence) to copy the metal ions residue(s) as a rigid body into the model.