MDVWhole can be used to make broken segments over PBC whole. All you need is a coordinate and or trajectory file. It does not make any copies of the box and can handle an arbitrary amount of consecutive PBC crossings. Making things whole runs near real time on a laptop for systems including up to millions of particles.
Testing is still ongoing (beta), but functionality can be expected to give the right results. We will write a short paper to explain our methodology. This tool can be used for all atom and coarse-grained systems.
Cheers and feel free to leave a comment here or at github if you have any issues or requests,
Bart