Select a bond type using the Bond toolbar button or by shortcut .
To link two existing atoms, select a bond type, click on one then drag the cursor to the other.
To draw a bond from a single atom, simply click the atom. A carbon atom is added at the other end of the bond.
Marvin allows you to draw a bond between any two atoms in the molecule. Valence errors are highlighted (if that option is enabled).
If you add a bond to empty canvas space, a carbon atom is added to each end of the bond.
To change the orientation of a wedge bond click with the corresponding wedge bond tool on the bond.
To change the order of bonds which cross each other : Select the bond to move to the front and go to Contextual menu < Arrange < Bring to Front. The selected bond now is drawn in front of all other bonds (or objects). Similarly, the Send to Back option paints the bond behind other bonds(or objects) .
Double bonds can have one of three alignments relative to the chain: above, centered and below
To change the alignment click the double bond tool and click on the existing bond as many times as necessary.
Further bond types applied in Marvin:
multi-center bond (For details see the Coordination compounds section.)
position variation bond (For details see the Markush structure section.)
You can replace any bond in the molecule by placing a new bond type on top of it.
Bond types can also be changed using the Bond pop-up menu .
Single bonds can be changed to double or triple by left-clicking on them
Additionally, you can change a bond, selecting it and use the following keys shortcut.
|Single Up or Down|
|Double Cis or Trans|
|Double C/T or Unspec|
|Single or Double|
|Single or Aromatic|
|Double or Aromatic|
|5||Single up bond (active only in 2D)|
|6||Single down bond (active only in 2D)|
|7||Single up or down bond|
|12||Single or double bond|
|14||Single or aromatic bond|
|24||Double or aromatic bond|
It is located in the Bond menu, on the Tools toolbar and in the Bond pop-up menu by default.
Activate the tool, click on a bond and it will be changed to bold.
In case of single, double, or aromatic bond clicking again you can reestabilish the original bond.
Aromatic bonds has four representations:
bold aromatic up,
reversed bold aromatic up,
and single .
You can make the selected bond hashed: Choose the icon from the Tools toolbar or the Bond > Hashed menu option. It retains the original single bond type.