If I understand your purpose correctly, I would do the following:
- Have the nanocone in the Builder.
- Go to Coordinate tools -> Translate
- Select the desired distance in the c-direction, check the Copy-box and click Apply
- Go to Coordinate tools -> Rotate
- Choose the rotation axis (I assume z) and the rotation angle and click Apply
This will give the following, for a rotation angle of 90 degrees: