As mentioned earlier, you can save structures relative to each other in Chimera. First, open both structures in Chimera. Then, follow Tools → Structure Comparison → MatchMaker.

This brings up the MatchMaker panel (see the image below). On the left, you’ll select one structure as the reference, and you’ll choose the ones to match on the right.

The MatchMaker window has reference structures to the top left and structures to match on the top right. Then there are a bunch of options for matching things. The same thing should not be selected for both the reference and the structure to match.
The MatchMaker screen, which allows you to align sequences and then save their coordinates relative to each other.

Once you’ve hit “apply,” they’ll be matched and oriented to the reference you selected. You can then save them through File → SavePDB. Highlight the one to save, and then select the correct option under “Save relative to model,” depending on what you want.