It is possible to associate atoms in reactants to products with atom-to-atom mapping.
Unlike atom indexes, map labels are constant and cannot be changed when the molecule is altered.
The various mapping tools that are available through Structure > Mapping can be used to map a drawn reaction either manually or automatically.
To see the map labels, the View > Advanced > Atom Mapping option must be turned on.
It is possible to 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.
For more information about alternative manual mapping methods, see the following sections:
If the first atom does not have an atom map number, but the second atom has one, both atoms have to be numbered with the smallest integer which is 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 clicking Structure > Mapping > Unmap Atoms, or by typing m0 for the selected atoms.
It is possible to map reaction automatically by using the automap function which is available through Structure > Mapping .
The following automatic mapping methods are available in MarvinSketch:
Complete: All atoms are mapped.
Changing: Only those atoms 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-style mapping). A reaction atom is considered matching if it is not an orphan or a widow atom, that is, it exists on both sides of the reaction.