Trajectory convert method

Dear OpenFE Developers.

Thank you for your useful code to execute RBFE Protocol. I use OpenFE everyday.

I want ot ask about the best way to obtain well-aligned trajectory.
Previously, I asked the way to split hybrid ligand to individual ligand (https://github.com/OpenFreeEnergy/openfe/issues/1509).
Since then, I have tried to obtain well-aligned trajectory based on protein in complex leg (to discuss experimental scientist).
However, I couldn't reach best protocol to convert trajectory of complex leg (e.g. part of the divided chain jumps over the periodic boundary).
I use trajectory convert using MDAnalysis and MDTraj.

Are there any nice method to obtain trajectories easy to see or developing such method?
(In the first place, how does your developmental group visualize the trajectory?)

I'm sorry to trouble you, but I would appreciate it if you could let me know.
Best regards.