-rotate <axis> <angle>
or
-rot <axis> <angle>
This option allows to rotate the system around a cartesian axis.
The user has to provide the axis of rotation (has to be x, y or z -referring to cartesian axes), and the angle of rotation (in degrees).
Default is <angle> = 0 (i.e. the system is not rotated at all).
pikashu initial.cfg final.xyz -rotate x 45
This will rotate the system by 45 degrees around X.