---
title: Measure in 3D
url: https://www.moldraw.com/docs/analyze/how-to-measure-bond-lengths-and-angles-in-3d/
section: Analyze and 3D
updated: 2026-10-20
publisher: LabCanvas
---

# Measure in 3D

> Click Measure (the ruler) in the 3D toolbar and pick Distance, Angle or Torsion. Click 2, 3 or 4 atoms in the 3D model. The value appears on the model in angstroms or degrees.

The measure tool reads the 3D model in the [3D panel](https://www.moldraw.com/docs/analyze/how-to-view-molecules-in-3d/). Values stay on the model until you clear them or the structure changes.

## Measure a bond length

1. Draw the molecule and wait for the 3D model to finish building.
2. Click **Measure** (the ruler icon) in the 3D toolbar.
3. Click **Distance**.
4. Click the first atom, then the second atom in the 3D model.
5. The distance shows on a dashed line between them, for example 1.54 Å.
6. Click **Done** in the hint box, or press `Esc`, to stop measuring.

## The three measurements

| Measure | Atoms to click | Result | Where the value sits |
| --- | --- | --- | --- |
| **Distance** | 2 | Bond length or any atom to atom distance, in Å with 2 decimals | Middle of the line |
| **Angle** | 3 | Angle at the middle atom, in degrees with 1 decimal | Inside the angle |
| **Torsion** | 4 | Dihedral angle along the middle bond, from -180° to 180° | Middle bond |

The two atoms do not need to be bonded. Use **Distance** for a hydrogen bond, a ring diagonal or a through space contact.

While you click, a hint box shows the tool and *Click atom 1 of 3*. Picked atoms get an orange halo.

## Fix a wrong click

- Click the last picked atom again to undo it.
- An atom you already picked in this measurement is ignored.
- Press `Esc` to stop. Atoms picked for an unfinished measurement are dropped.

## Clear measurements

Open **Measure** again and click **Clear measurement** (or **Clear 3 measurements**). Measurements also clear when the 3D model changes. That happens when you edit the 2D drawing, apply a conformer, run **MMFF94** or click **Calculate structure**.

## Measure in a better geometry

The values come from the 3D model MolDraw builds from your 2D drawing. For a closer match to real bond lengths and angles:

1. Open **More** (three dots) in the 3D toolbar.
2. Click **MMFF94** to minimize the structure.
3. Measure again. Earlier values are cleared because the pose changed.

You can also pick a pose from **Conformers** first. Torsion angles change a lot between conformers. See [3D looks, styles and surfaces](https://www.moldraw.com/docs/analyze/3d-viewer-styles-looks-and-molecular-surfaces/) for the conformer gallery.

## Use the values in a figure

Measurement labels are part of the 3D image. **PNG** and **JPG** exports from the 3D toolbar include them. Mesh files like GLB and OBJ do not. See [3D export](https://www.moldraw.com/docs/analyze/how-to-export-3d-models-glb-obj-with-a-color-legend/).

## Tips

- Turn on **Symbols with numbers** under **Labels and legend** (the tag button). You then see C1, C2, O3 and know which atoms you measured.
- Rotate the model so the atoms do not overlap before you click.
- For Newman views of a torsion, use the [chair and Newman projection tool](https://www.moldraw.com/tools/free-chem-tools/chair-conformation-newman-projection.html) and the [conformation guide](https://www.moldraw.com/blog/chair-conformation-newman-projection-guide.html).
- For predicted shapes from VSEPR, try the [VSEPR geometry calculator](https://www.moldraw.com/tools/free-chem-tools/vsepr-molecular-geometry-calculator.html).

## Common problems

| Symptom | Fix |
| --- | --- |
| The ruler is greyed out | There is no 3D model yet. Draw a structure and wait for it to build. |
| Clicking an atom selects it in 2D instead | No measure type is active. Open **Measure** and pick one first. |
| A hydrogen cannot be picked | Hydrogens are hidden. Tick **Show hydrogens** under **Display**. |
| Values disappeared | The 3D model changed. Measure again. |

## Questions and answers

**How do I measure a bond angle in MolDraw?**
Click Measure in the 3D toolbar, pick Angle and click three atoms. The middle atom is the vertex.

**What units does the MolDraw measure tool use?**
Distances are in angstroms with two decimals. Angles and torsions are in degrees with one decimal.

**Can I measure a dihedral angle?**
Yes. Pick Torsion and click four atoms in a row. The value is signed, from -180 to 180 degrees.

**Are the bond lengths experimental?**
No. They come from the 3D model MolDraw computes. Run MMFF94 in the More menu for a refined geometry.

## Practice it

- Interactive lesson: [How to view a molecule in 3D](https://www.moldraw.com/learn/how-to-view-a-molecule-in-3d/)

## Related pages

- [3D viewer](https://www.moldraw.com/docs/analyze/how-to-view-molecules-in-3d/)
- [3D looks, styles and surfaces](https://www.moldraw.com/docs/analyze/3d-viewer-styles-looks-and-molecular-surfaces/)
- [Export 3D models](https://www.moldraw.com/docs/analyze/how-to-export-3d-models-glb-obj-with-a-color-legend/)
- [Names, formula and properties](https://www.moldraw.com/docs/analyze/how-to-find-iupac-name-molecular-formula-and-weight/)