you can try Atomsk

http://atomsk.univ-lille1.fr/tutorials.php

I interested.....

We have MedeA plugged in with LAMMPS, so use its inteface to build interfaces and simulate.

LAMMPS lattice command has a keyword "orient" to rotate the lattice

https://lammps.sandia.gov/doc/lattice.html

You just need to define the crystallographic direction of each coordinate.

https://en.wikipedia.org/wiki/Miller_index

You must determine the size of the supercell to ensure the periodicity of the rotated lattice.