Export 3D models
Short answer: Click Export (the download icon) in the 3D toolbar and pick GLB, OBJ, PNG, JPG, SDF, XYZ or X3D. To add an element colour legend or atom labels, use Labels and legend (the tag button) first. The legend and labels appear in PNG and JPG images only.
3D export saves what the 3D panel shows. For 2D files such as SVG, PDF and MOL, see download and file formats.
Export a 3D model#
- Set up the view: look, style and rotation. See 3D looks, styles and surfaces.
- Optional: click Labels and legend (tag icon) and turn on the legend or atom labels.
- Click Export (download icon) in the 3D toolbar.
- Pick a format. The file downloads at once.
Exports need a free MolDraw account. If you are not signed in, MolDraw asks you to sign up first. See sign in and create a free account.
Formats#
| Format | What you get | Legend and labels |
|---|---|---|
| GLB | One binary 3D mesh file, ball and stick, with one coloured material per element | No |
| OBJ | Two files: the .obj mesh and a .mtl file with the colours |
No |
| PNG | Image of the current view, transparent background by default | Yes |
| Transparent PNG | Switches PNG transparency on or off, then downloads a PNG | Yes |
| JPG | Image of the current view on a white background | Yes |
| SDF | 3D coordinates as a molfile, for other chemistry software | No |
| XYZ | Plain atom coordinates | No |
| X3D | 3D scene file for web and X3D viewers | No |
The file name comes from the molecule name shown in the panel, for example caffeine.glb. With no name it is molecule.
Note
The Transparent PNG row is highlighted while transparency is on. Clicking it flips the setting and downloads a PNG with the new setting. Plain PNG keeps whatever setting is active.
Labels and legend#
Click the tag button in the 3D toolbar.
| Option | What it does | Default |
|---|---|---|
| Element colour legend | A key in the corner that shows which colour is which element, in the order C, H, then A to Z | Off |
| No atom labels | No text on atoms | Yes |
| Element symbols | C, H, O on every atom | |
| Symbols with numbers | C1, C2, O3 in file order |
Hydrogen labels follow Show hydrogens. Measurement values from the measure tool are also drawn into PNG and JPG files. MolDraw remembers your legend and label choice in this browser.
GLB and OBJ in other apps#
GLB and OBJ files are ball and stick meshes in angstrom units. Each element has its own material, named after the element, for example C (Carbon). The colours match the look you picked.
- PowerPoint: insert the GLB as a 3D model. You can rotate it on the slide.
- Affinity: place the GLB in your design.
- Blender: import the GLB, or the OBJ with its MTL file. Each element is a separate material, so you can restyle all carbons at once.
- Web viewers and Windows 3D Viewer: open the GLB directly.
Tip
Keep the .obj and .mtl files in the same folder. Without the MTL file the model opens grey. Your browser may ask once to allow two downloads.
Mesh files have no text. For a colour key on a slide, export a PNG with Element colour legend on. Place it next to the model, or build the key from the material names.
Common problems#
| Symptom | Fix |
|---|---|
| A sign up window opens instead of a download | Exports need a free account. Sign in, then export again. |
| The PNG has a background | Transparency is off. Click Transparent PNG once. |
| The legend is missing from the GLB | GLB, OBJ and X3D are meshes only. Use PNG or JPG for the legend. |
| The model in Blender is very large | One angstrom is written as one metre. Scale it down. |
| No 3D structure to export | Wait for the 3D model to build, or click Calculate structure in More. |
Questions and answers
How do I export a molecule as a 3D model for PowerPoint?
Click Export in the 3D toolbar and pick GLB. Insert the GLB file in PowerPoint as a 3D model.
Does the GLB export include the colour legend?
No. The legend and atom labels are drawn only into PNG and JPG images. GLB and OBJ files carry one material per element instead.
Why does my OBJ file open without colours?
The colours are in the separate MTL file. Keep the .obj and .mtl files in the same folder.
How do I add atom numbers to a 3D image?
Click the tag button in the 3D toolbar and pick Symbols with numbers. Then export PNG or JPG.
Can I export 3D coordinates?
Yes. Pick SDF for a 3D molfile or XYZ for plain coordinates.
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