| -generate 5,7 | Generate new molecules downwards and upwards. |
| -rename D | Rename molecules from the given letter. |
| -verbose 7 | Verbosity of output. |
| -origin 10,-10,20 | Origin for rotation (default 0,0,0, can be "center" for COM). |
| -helix 25.3,67.1 | Helical rise and angle. |
| -reference 0,1.5,-0.2,35 | Reference symmetry axis and rotation angle (default 0,0,1,0). |
| -parameters parm.star | Atomic properties parameter file (default atom_prop.star). |