You can move or rotate a selected structure.

Select the part of the structure you wish to move and to

Move the selection:

1. Move the mouse pointer toward the center of the selected structure until a blue rectangle appears.(You can also use the Space key to change between transformation modes.)

2. Translate the selection by dragging the mouse.

Rotate the selection:

1. Move the mouse pointer toward the outline of the molecule until a blue gear appears.(You can also use the Space key to change between transformation modes.)

2. Rotate the selection by dragging the mouse.

Rotate the selection in 3D:

Rotation in 3D of the following structural parts is possible

• all compounds on the canvas,

• selected fragments,

• selected groups.

Rotation of all compunds on the canvas in 3D can be accomplished by the View > Mouse mode > Rotate in 3D menu option.
The axis of the 3D rotation for selected objects can be determined in the Edit > Transform > Rotate in 3D menu (or from the contextual menu) by choosing from the following list:

• Around an arbitrary axis defined by two atoms: in this case you are asked to select the atoms prior to the rotation.

• Around x axis: horizontal axis in the plane of the canvas

• Around y axis: vertical axis in the plane of the canvas

• Around z axis: axis perpendicular to the plane of the canvas

• Free 3D rotation: the rotation follows the movement of the mouse (click&drag).

• (Note: 3D rotation mode until version 5.3.x: pressing the Space key 3 times initiates the free 3D rotation.)

• Group Rotate: available only for a selected group in a molecule. The connecting bond(s) is recognized between the selected and unselected parts of the structure and selects the rotation axis accordingly.

The rotations are visualized by the fog effect: parts of the molecule behind the canvas are of lighter colour than the parts on the canvas. To see best the 3D view, use white background (View > Colors > White Background).

Customized tool: 3D plane:

1. Select 3 atoms in the molecule.

2. Click the 3D Plane button or select Edit > Transformation > 3D Plane.

The selected 3 atoms will lie in the plane of the canvas. The coordinates are changed, not only the view of the structure