[modeller_usage] Adding missing residues to PDB with two chains

Hi, I am new to Modeller. Here, I am trying to add missing residues in my PDB. My PDB has two chains A and B. I checked the tutorial and mailing lists where they talk about PDB with single chain. So, how can I get an .ali file for my protein and how should I label the residues to be inserted.

Thank You. Anjela Manandhar