Moving&Rotating

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 images/download/attachments/46805324/rotate-mode24.png 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

Currently 3D coordinates of brackets (e.g. monomer, component type groups) are not correctly updated when rotating the molecule in 3D mode.