Bond-Centric Manipulation Tool#

The Bond-Centric Manipulation Tool is a powerful tool that allows you to focus on a specific bond and change its length and the surrounding angles, while keeping the rest of the molecule the same.

Starting with the basics:#

  • To begin using the bond centric manipulate tool, click on a bond within your molecule.

  • Clicking on a bond and dragging your cursor allows you to adjust the plane.

  • If the “Show Angles” box is checked, the angles from the selected bond to all adjacent bonds are displayed.

  • If the “Snap-to Bonds” box is checked you’ll notice that the plane changes from yellow to blue as it’s rotated. A yellow plane indicates that an adjacent bond is in line with the plane. If the plane depicted is blue, the plane is not in line with any adjacent bonds.

  • “Snap-to Threshold” determines how many degrees away a plane has to be to snap to an adjacent bond plane.

    • For example, the “Snap-to Threshold” shown below is 10 degrees. Therefore if the plane being rotated comes within 10 degrees of an adjacent bond, it will snap to the adjacent bond’s plane.

    • Changing the Snap-to Threshold to 90 degrees is a quick trick for the rotating plane to only snap to adjacent bond planes.

Adjusting Bonds and Torsion Angles#

Once a plane is selected the atoms on either end of the plane can be manipulated, by left-clicking on the atom and dragging. The displayed angles will automatically adjust, and the selected bond will not change in length.

Left-clicking on a substituent, or in this case a hydrogen bonded to one of the selected carbon atoms will allow you to adjust the torsion angle.