Examining antibody - target interactions in PyMOL
Multiple structures may be read into a given session using the following for each pdb:
File -&gt; Open

In the narrative below, the reference antibody has the name AAA and the second antibody has the name BBB. The heavy and light chains have pdb chain IDs A and B, respectively. Adjust those as needed.
Whole molecule overlay
Make visible the reference and the moving molecules.
From the menu item next to the BBB molecule name (right panel), select:
A -&gt; align -&gt; to molecule (*/CA) -&gt; Object: AAA

Antibody's variable domain overlay
I think it may be more helpful to align the variable domains than the whole antibodies or Fabs. Typing the following on the command line is a temporarily adequate way to align proteins:
align BBB and chain A+B and res 1:109, AAA and chain A+BL and res 1:109