Mapping Reactions

In reactions you can associate atoms in reactants to products with atom-atom mapping.

Map labels are constant, unlike atom indexes, which can change when the molecule is altered.

You can find in the Structure< Mapping submenu the Mapping tools allowing you to map a drawn reaction either manually or automatically.

Make sure that the Atom Mapping visibility option is selected in View > Advanced submenu.

Manual mapping

You can assign the same free map number to atoms by selecting Insert Reaction Arrow from the Tools Toolbar then drawing the reaction arrow from the first atom to the second one.

You can also select a map number for an atom from

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.

Automatic mapping

You can map your reaction automatically with automap available from Structure< Mapping submenu .

Marvin offers 3 methods:.

  • Complete - all atoms are mapped

  • Changing - only those atom are assigned that have a changing bond. The bond can be created, deleted or its order can be changed. Orphan and widow atoms are included.

  • Matching - maps all matching atoms in the reaction (Daylight sytle mapping). A reaction atom is considered matching if it is not an orphan/widow atom: it exists on both sides of the reaction.