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.
Manual mapping
The arrow tool provides the easiest way to map manually the corresponding reactant and product atoms.
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Sequential mappig
Select the arrow tool and drag it to the corresponding product atom.The smallest possible map number is added to both atoms marking, that they represent the same atom on the two sides of the reaction scheme.
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Mapping with a user-defined atom number
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Type m and the desired number ("m8", for example, and click on an atom. Atom map 8 is assigned to that atom).
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Select the arrow tool and drag it to its counterpart. The same number (8) 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.
Automatic mapping
You can map your reaction automatically with automap available from Structure< Mapping submenu .
Marvin offers 3 methods:.
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Complete - all atoms are mapped
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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.
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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.