Modifying bonds
General bond options
The following options are found under the Builder menu:
| Options | Explanation |
| Create bond | Select two atoms to be bonded. |
| Set bond order | Select two atoms and choose the bond order. The same operation can be done from the builder palette. |
| Rotate around bond | Select two atoms to choose the bond around which to rotate. The atom that is clicked first, is treated as connected to the parent substructure, and the second atom belong to the substructure that is rotated. In addition, there is an option to enable dynamic tracking of steric clashes. Rotation is achieved by dragging the mouse right or left in the display are. Mving the mouse to the righ corresponds to the clockwise rotation when viewed along the axis of rotation in the direction of the arrow. |
| Break bond | Select two atoms that are connected by a bond that needs to be broken. |
Rotating a functional group
around a specified bond while checking dynamically for steric clashes.
Detect missing bonds
This operation scans through the structure and finds isolated atoms that are close enough to other atoms that they may in fact be covalently bonded. This feature can be used for some files that are missing bonding information or the information has been misinterpreted when loaded.