Measure in 3D
Short answer: 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. Values stay on the model until you clear them or the structure changes.
Measure a bond length#
- Draw the molecule and wait for the 3D model to finish building.
- Click Measure (the ruler icon) in the 3D toolbar.
- Click Distance.
- Click the first atom, then the second atom in the 3D model.
- The distance shows on a dashed line between them, for example 1.54 Å.
- 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:
- Open More (three dots) in the 3D toolbar.
- Click MMFF94 to minimize the structure.
- 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 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.
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 and the conformation guide.
- For predicted shapes from VSEPR, try the VSEPR geometry calculator.
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.
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