Did you make sure that the two proteins use different chain labels? Once you merge the two proteins into one object, they can no longer be distinguished if they both use the same chain label. You can change the chain label by using the "alter" command: https://pymolwiki.org/index.php?title=Alter&redirect=no

If you only need to identify the contact residues, you can do this with a distance selection:

select IFresiduesA, br.(ObjectA within 3.5 of Object B)

select IFresiduesB, br.(ObjectB within 3.5 of Object A)

(a cut-off of 3.5Å gives you VdW contacts in structures that do not contain explicit hydrogens)

You can then list the contact residues by

list=[]

iterate (IFresiduesA and name ca),list.append((chain,resi,resn))

print list

Annemarie Honegger That fixed the problem. Thank you very much for your guidance.