3D looks, styles and surfaces
Short answer: In the 3D panel toolbar, click Display (the circle icon) to pick a Look and a Style. Click Surfaces (the layers icon) to add a VDW, MS, SAS or SES surface. Gloss and Ball & stick are the defaults.
This page lists every display option in the 3D panel. For opening the panel, rotating and 3D Clean Up, see 3D viewer.
Where to find it#
The 3D toolbar is a small island on the side of the 3D panel. It has these buttons:
| Button | Opens |
|---|---|
| Display (circle) | Show hydrogens, Look and Style |
| Surfaces (layers) | Surface type, opacity and colour |
| Measure (ruler) | Distance, angle and torsion. See measure in 3D. |
| Labels and legend (tag) | Colour legend and atom labels. See 3D export. |
| More (three dots) | Conformers, MMFF94 and Calculate structure |
| Export (download) | GLB, PNG, JPG, SDF, XYZ, X3D, OBJ |
On a phone, tap the 3D pill in the panel. The same buttons open in a 3D controls sheet.
Change the look and style#
- Click Display in the 3D toolbar.
- Under Look, click a sphere preview.
- Under Style, pick how atoms and bonds are drawn.
- Tick or untick Show hydrogens.
MolDraw remembers your look and style in this browser.
Looks#
| Look | What it looks like |
|---|---|
| Gloss (default) | Glossy, candy-like spheres with crisp highlights |
| Studio | Clean studio light with gentle gloss and soft contact shadows |
| Soft | Matte finish with deep, soft shadows |
| Toon | Cel shading with clean ink outlines |
| Clay | White architectural model with soft shadows |
| Flat journal style with fine outlines | |
| Neon | Dark stage with glowing rims |
Exports and the conformer preview use the same look you pick here.
Styles#
| Style | What it shows |
|---|---|
| Ball & stick (default) | Atoms as balls, bonds as sticks |
| Spacefill (CPK) | Atoms at their van der Waals size |
| Stick | Bonds as cylinders only |
| Line | Thin wireframe bonds |
| Cross | Small crosses at atom centres |
Add a molecular surface#
- Click Surfaces in the 3D toolbar.
- Under Type, pick a surface.
- Drag Opacity to see the atoms through it.
- Under Color, pick how the surface is coloured.
- Pick Off to remove it.
| Type | Meaning |
|---|---|
| VDW | van der Waals surface |
| MS | Molecular surface |
| SAS | Solvent-accessible surface |
| SES | Solvent-excluded surface |
| Color | What it does | Default |
|---|---|---|
| Solid color | One colour you pick for the whole surface | |
| Color by atom | Element colours on the surface | Yes |
| MEP (charges) | Red is electron-rich, blue is electron-poor | |
| Volumetric | Colours from a Gaussian cube file you load with Load .cube |
Opacity starts at 75% and goes from 10% to 100%.
Note
MEP (charges) is an estimate from atomic partial charges. It is good for polarity and hydrogen bond sites, not for exact energies. The MEP plugin turns it on in one click and pins the legend. For the theory, read bond polarity and dipole moments.
Conformers and energy#
Open More for the calculation tools.
- Conformers opens the Conformer gallery. Pick Max conformers (6, 12, 18 or 24; 12 by default), click Regenerate, pick a pose and click Apply to 3D viewer. It works up to 80 heavy atoms. Larger molecules show Conformers (N/A).
- MMFF94 minimizes the current 3D pose with the MMFF94 force field. The energy shows at the bottom of the panel in kcal/mol.
- Calculate structure rebuilds the 3D model from your drawing. Use it when the model looks flat or stops building.
Common problems#
| Symptom | Fix |
|---|---|
| 3D view unavailable message | Turn on graphics acceleration in your browser settings, restart the browser and click Retry 3D. Close other 3D tabs. |
| The surface takes a moment | Surfaces are computed in the background. Large molecules take longer. |
| Hydrogens vanish from the surface | Show hydrogens also controls the surface. Tick it again. |
| Conformers stay greyed out | The molecule has more than 80 heavy atoms. Use Calculate structure. |
Questions and answers
How do I change the 3D style to spacefill in MolDraw?
Click Display in the 3D toolbar and pick Spacefill (CPK) under Style.
What is the default 3D look in MolDraw?
Gloss. You can switch to Studio, Soft, Toon, Clay, Print or Neon under Display, Look.
What is the difference between SAS and SES surfaces?
SAS is traced by the centre of a solvent probe rolling over the atoms. SES is the surface the probe cannot enter, so it sits closer to the atoms.
How do I show an electrostatic potential surface?
Click Surfaces, pick a surface type and choose MEP (charges) under Color. Red is electron-rich and blue is electron-poor.
Why is the conformer gallery not available?
It works for molecules up to 80 heavy atoms. For larger molecules, use Calculate structure in the More menu.
Last updated: