---
title: Check a structure
url: https://www.moldraw.com/docs/analyze/how-to-check-a-structure-for-valence-errors/
section: Analyze and 3D
updated: 2026-10-20
publisher: LabCanvas
---

# Check a structure

> 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

1. Draw or open your structure in the [editor](https://www.moldraw.com/).
2. Click **Chemistry** in the top bar, then click **Check structure**.
3. Read the note under the search box. It says **Structure check: no issues** or **Structure check: 2 issues (see Info)**.
4. If there are issues, select the molecule. The **Info** panel opens with a **Structure check** list.
5. 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](https://www.moldraw.com/docs/ai/how-to-use-the-ai-chemistry-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](https://www.moldraw.com/docs/teaching/how-to-show-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](https://www.moldraw.com/docs/drawing/how-to-add-atom-labels-and-r-groups/). |

For the theory behind octets and formal charge, read the [formal charge and hybridization guide](https://www.moldraw.com/blog/formal-charge-hybridization-guide.html).

## 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.

## Related pages

- [Show errors and error tooltips](https://www.moldraw.com/docs/teaching/how-to-show-chemistry-errors-and-error-tooltips/)
- [Names, formula and properties](https://www.moldraw.com/docs/analyze/how-to-find-iupac-name-molecular-formula-and-weight/)
- [Lone pairs, radicals and charges](https://www.moldraw.com/docs/drawing/how-to-add-lone-pairs-radicals-and-formal-charges/)
- [3D viewer](https://www.moldraw.com/docs/analyze/how-to-view-molecules-in-3d/)