Not sure how you can get a distorted nanotube in the Nanotube Builder, since it's supposed to build perfect tubes only
But I guess you can manipulate it slightly.
Anyway, you can quite easily strip the unit cell from the configuration by dropping it from the Nanotube Builder onto the Script Editor. There, remove all the lines defining the PeriodicAtomConfiguration at the bottom, and replace them with
molecule = MoleculeConfiguration(
elements,
cartesian_coordinates=coordinates
)
Then you should be able to drop the system to the Molecular Builder for further manipulations.
Thus, in effect, remove the 4th line from the bottom (containing just "unit_cell,") and replace the line
periodic_atom_configuration = PeriodicAtomConfiguration(
with
molecule = MoleculeConfiguration(