Atom mapping with Automap
Short answer: Draw the reactants, a reaction arrow and the products. Press Ctrl+K, type Automap and pick Automap reaction atoms. Each atom gets a number, and the same number marks the same atom on both sides of the arrow.
Atom mapping links each atom in the starting materials to the same atom in the products. It shows which bonds break and form. MolDraw finds the map for you with Automap.
- Draw the reactants on one side of the canvas.
- Add a reaction arrow with the Reaction Arrow tool. Use Straight or another arrow from the Scheme group.
- Draw the products on the other side.
- Press Ctrl+K (Cmd+K on a Mac) to open the command palette.
- Type Automap and pick Automap reaction atoms.
A short message tells you how many atoms were mapped, for example Automap: 12 atoms mapped.
Other ways to run it#
- AI chat: open AI and ask it to map the reaction atoms. The assistant runs the same Automap. See AI assistant.
- Undo: Ctrl+Z removes a map you do not want.
What the numbers mean#
Each mapped atom shows a small number in an amber circle at its upper left. Atoms with the same number on both sides are the same atom. An atom with no number has no partner. This often means it is a leaving group, a by-product you did not draw, or a reagent.
Hydrogens are not numbered.
The numbers are part of your drawing. They show in PNG, SVG and PDF downloads. MOL files keep them in the atom mapping column, so other chemistry software can read them. See Download and file formats.
Requirements#
| Needed | Why |
|---|---|
| At least one reaction arrow | Automap uses the first arrow that splits the drawing. |
| A splitting arrow kind | Straight, Curved, S-curve and Retro arrows count. Equilibrium, Half eq., Resonance, Path 90°, Row wrap, Cycle arc and curved electron arrows do not. |
| Structures on both sides | The side nearer the arrow tail is the reactants. The other side is the products. |
| The same atoms on both sides | Draw every product you want mapped. Missing atoms stay unmapped. |
Clear the maps#
- Press Ctrl+Z right after Automap.
- Run Automap again. It clears the old numbers on both sides before it writes new ones.
- Ask the AI chat to clear the atom maps.
Common problems#
| Message or symptom | Fix |
|---|---|
| Automap needs reactants and products separated by a reaction arrow | Add a Straight arrow between the two sides. Equilibrium and mechanism arrows do not count. |
| Automap: no maps assigned | Check that the products contain the atoms of the reactants, and that both sides are complete structures. |
| Some atoms have no number | The atom has no partner on the other side. Draw the missing by-product, or leave it unmapped. |
| Wrong atoms are paired | Keep the reactants and products clearly on two sides of the arrow, then run Automap again. |
To draw the arrows that explain each step, see Curved arrow mechanisms.
Questions and answers
What is atom mapping in a reaction?
Atom mapping gives each atom a number that stays the same from reactant to product. It shows where every atom ends up and which bonds change.
Where is the Automap button in MolDraw?
Automap is a command. Press Ctrl+K or Cmd+K, type Automap and pick Automap reaction atoms. You can also ask the AI chat to map the reaction.
Do atom map numbers show in my exported image?
Yes. The numbers are part of the drawing, so they appear in PNG, SVG and PDF files. Undo the Automap before you export if you do not want them.
Does Automap work with an equilibrium arrow?
No. Automap needs a Straight, Curved, S-curve or Retro arrow to split the reactants from the products.
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