The first thing you have to do is combine the two models into one. Do this by going to the Model Panel and choosing “copy/combine…” on the right. In the resulting dialog, make sure to check the “Close source models” box.

You then have two options to change the chain IDs. The most straightforward one is to simply save a PDB file and hand edit the chain ID column from blank to the proper chain ID for those residues that are missing IDs. Tedious but simple.

The other option is to select the parts missing chain IDs and using a Python script that I have attached to set the chain IDs. First you would select the parts you want to get chain ID ‘A’ and then run the script (simply by opening it). Then you would select the parts you want to get chain ID B and edit the first line of the Python file to change ‘A’ to ‘B’ and then run the script. The simplest way to do the select is to again use the Model Panel and pick “select chains…” on the right. Use the right side of the resulting dialog to select by connectivity. You will be able to select the entirety of chain A (and later chain B), including its glycans. The you can use the script to set the selection to the proper ID.

This will leave the ligand with no ID because it isn’t connected to anything. Nonetheless, you can then select it with the command (Favorites→Command Line) “sel ~:.A-B” (i.e. select everything that doesn’t have chain ID A or B). Then you can again use the script to set its ID to whatever you want.