MarvinSketch allows you to set a map label on any atom in the molecule.

Map labels are useful because they remain constant, unlike atom indexes, which can change as the molecule is altered. Atom mapping can be very useful when drawing reactions.

It allows you to specify that specific reactant atoms will become specific product atoms.

The arrow tool provides the easiest manual way to map manually the corresponding reactant and product atoms.

• Sequential mappig

Select the arrow tool and drag it to the corresponding product atom.The same, smallest possible map number is added to both atoms marking, that they represent the same atom on the two sides of the reaction scheme.

• Mapping with a user-defined atom number

1. Type m and the desired number 8, for example, and click on an atom. Atom map 8 is assigned to that atom.

2. Select the arrow tool and drag it to the corresponding product atom. The same number will be added to the Product.

If the first atom does not have atom map number, but the second atom has one, both atom has to numbered with the smallest the smallest integer which bigger than zero and does not belong to any atom on the canvas yet.

Map numbers of the selected atoms can be removed by the Structure > Mapping > Unmap Atoms menu item, or by typing m0 for the selected atoms.

Similar tool "Manual Atom Map" can be added by customization.

Marvin contains an automapper tool as well (available as Structure > Mapping > Map Atoms) assigning map numbers to all selected atoms of a reaction automatically.