MarvinSketch allows you to draw reactions in your molecule by placing a reaction arrow.
You can place the reaction arrow in any position, pointing in any direction.
The structures before the arrow will be considered Reactants, structures along the arrow Agents, and structures after the arrow as Products.
Mapping
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.
You can assign the same free map number to both of these 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
- Atom pop-up menu or use
- shortcuts
M1, M2, to assign map labels
M0 to remove map labels
M= or M+ to assign unique map numbers
Alternatively, you can use the built-in automapper tool of Marvin, available from the Structure >Mapping > Map Atoms menu or from the Selection Pop-up menu, to assign map numbers to atoms in a reaction automatically.