Bond Pop-up Menu

The bond pop-up menu appears when you right-click on a bond within the molecule. It allows you to make changes to the selected bond. It contains options for bond-specific activities that also can be accessed from the Bond Menu.

Menu item



Changes the selected bond type to Single. Changes the type of the selected bond. For more information regarding bonds, see Draw Bonds.


Thickens the selected bond.


Changes the selected bond hashed.

Topology > None

Removes defined bond topologies.

Topology > In Ring

The specified bond must be in a ring to score a hit.

Topology > In Chain

The specified bond must be in a chain to score a hit.

Reacting Center > None

Removes added bond property.

Reacting Center > Center

Specifies that the bond takes part in the reaction.

Reacting Center > Make or Break

The assigned bond can form or disappear in the reaction.

Reacting Center > Change

The assigned bond remains and can alter during the reaction.

Reacting Center > Make and Change

The assigned bond can form, break, or change its type during the reaction.

Reacting Center > Not Center

The assigned bond can not be the reaction center.

Stereo Search

Uses stereo configuration of the specified double bond when the molecule is used as a query.

Arrange > Bring to Front

Brings the selected bond in front of the others.

Arrange > Send to Back

Sends the selected bond to the back of the others.

Align > Horizontally

Orients the selected bond horizontally.

Align > Vertically

Orients the bond vertically.


Creates a custom Substructure Group (S-group)

Add > Explicit Hydrogens

Adds explicit H atoms.

Add > Map Atoms

Maps atoms.

Add > Data

Attaches data

Add > Multi-Center

Adds a multi-center attachment point representing a group of atoms.

Add> Position Variation Bond

Create a variable point of attachment to represent a connection point to a group of atoms.

Remove > Explicit Hydrogens

Removes explicit H atoms.

Remove > Unmap Atoms

Unmaps atoms.

Transformation > Drag selection

Enables you to drag the selected bond.

Transformation > Rotate in 3D

Options for rotation


Formats color, thickness, and length of the selected bond.

Add to My templates

Adds the bond to the Advanced Template Toolbar

Edit properties

Adds bond properties.