Check a structure
Short answer: Open the Chemistry menu in the top bar and click Check structure, or press Ctrl+K and type Check structure. A note under the search box says how many issues it found. Select the molecule and open Info to read each issue.
Check structure looks at everything on the canvas. It reports atoms with too many bonds, unusual formal charges and stereo bonds drawn to hydrogen. It does not change your drawing.
Run a structure check#
- Draw or open your structure in the editor.
- Click Chemistry in the top bar, then click Check structure.
- Read the note under the search box. It says Structure check: no issues or Structure check: 2 issues (see Info).
- If there are issues, select the molecule. The Info panel opens with a Structure check list.
- Fix the atoms in the list, then run the check again.
Other ways to start the check#
| Where | How |
|---|---|
| Top bar | Chemistry, then Check structure |
| Command palette | Press Ctrl+K (or Cmd+K on a Mac) and type check or valence |
| Phone or tablet | Tap the hexagon (Chemistry) button, then Check structure in the sheet |
| AI chat | Ask the AI assistant to check the structure |
The menu item is greyed out for a moment while the editor finishes loading. It does nothing on an empty canvas.
What the check reports#
Each line in the Structure check list starts with a type.
| Type | Example message | What it means |
|---|---|---|
| valence | C atom exceeds typical valence (6 > 4) | The bonds plus hydrogens on the atom add up to far more than normal. |
| charge | Unusual formal charge 3 on N | The charge is larger than +2 or smaller than -2. |
| stereo | Stereo bond attached to hydrogen | A wedge or hash bond touches an H atom. |
The valence limits used are H 1, B 4, C 4, N 3, O 2, halogens 1, P 5 and S 6. Other elements get a limit of 8. The check allows one bond more than the limit before it reports an issue. So it only flags clear errors.
Note
The list covers the whole canvas, not just the molecule you selected. Aromatic rings are checked in their Kekulé form, so a benzene ring drawn with a circle is fine.
Octet markers while you draw#
You do not need to run a check to see most valence errors. MolDraw never blocks a bond. Instead, an atom with too many bonds gets a small amber dot at its upper right corner. Unclear wedge or hash stereo gets an amber ring. If a bond type change overfills an atom, the note under the search box counts the atoms over normal valence.
These markers come from Settings, General, Show errors (on by default). Error tooltips shows the reason when you hover or tap a marked atom. The markers never appear in exports or print. See chemistry errors and error tooltips for the teaching options.
Common problems#
| Symptom | Fix |
|---|---|
| Check says no issues, but a carbon has five bonds | The check only flags clearly over-filled atoms. Look for the amber octet dot instead. |
| Issues are reported but Info shows nothing | Select at least one atom of the molecule. The list shows in Info only when something is selected. |
| Check structure is greyed out | The editor is still loading its chemistry tools. Wait a moment and open the menu again. |
| An atom label like Ph or COOH looks wrong | Expand or fix the label, then check again. See atom labels. |
For the theory behind octets and formal charge, read the formal charge and hybridization guide.
Questions and answers
Does Check structure fix errors for me?
No. It only lists the issues. You change the bonds, charges or labels yourself and run the check again.
What is the amber dot on an atom in MolDraw?
It is the octet marker. The atom has more bonds than its normal valence. Turn it off in Settings, General, Show errors.
Do the error markers show up in my exported image?
No. Octet dots and stereo rings are editor marks only. They never appear in PNG, SVG, PDF or print.
Can I check a reaction scheme?
Yes. The check runs over every structure on the canvas, including reactants and products.
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