With this free molecule builder, you can draw your structure, visualize in rotatable 3D and export as a PNG image or 3D object. The latter are the types of files I used to create animations in my YouTube videos.
Molecule Lab
Sketch molecules and see their approximate 3D geometry update automatically. No account required.
Loading the chemistry editor…
About accuracy, privacy and formats
Live 3D requires local runtime setup under WordPress Tools → Molecule Lab 3D. The preview updates about 2 seconds after the drawing becomes idle, not after every mouse movement. Kekule/Open Babel calculates approximate conformers; it may not generate all incomplete or chemically unusual drawings. PubChem lookup is an alternative for compounds with an existing 3D record; clicking that button sends your structure to PubChem through your site’s server. It is unsuitable for confidential or unpublished molecules.
2D file formats: The Kekule JSON project format can be saved and reopened in this tool, but it is not universal chemical JSON. SMILES import requires the locally installed Open Babel runtime to register a reader, while output uses Kekule’s writer; review chirality and bond geometry after conversion. The 2D MOL file reflects your sketch rather than the generated 3D structure. CDXML export is an initial subset for standard atoms, charges, isotopes and wedge/dash bonds; it rejects unsupported query features and should be checked by opening the file in ChemDraw before scientific use.
The PNG export captures the selected 3D orientation. You can choose original or larger rendering resolution and an optional transparent background. Large exports can use significant browser memory; export may not work in all browsers. The image excludes WordPress controls. Stereochemistry, protonation, tautomers, conformer choice and unusual chemistry must be independently checked. MOL/SDF preserves chemical connectivity and coordinates; GLB and OBJ + MTL are approximate colored ball-and-stick meshes for visualization, not chemically editable structures or automatically print-ready models. For OBJ, extract both the .obj and .mtl files from the ZIP to the same folder. Reactions, mixtures and macromolecules are not supported by this prototype.
How to draw a molecule online
If you need this spelled out, you probably have bigger things to worry about than chemistry, but here you go:
Step 1: Draw your structure of interest, including stereochemistry, just like you would in Chemdraw or any other tool.
Step 2: Click Visualize in 3D (if the live 3D preview is not enabled) to generate your model. Use the PubChem lookup to retrieve available 3D models of known compounds. There should be live 2D to 3D visualization of edits.
Step 3: Get a cheeky PNG image of the little fella. Then, rinse and repeat – or keep doing what you were doing…
I hope this allows you to appreciate the spatial arrangement of chiral centers, double bond geometry, cyclohexane chairs, fused-ring architectures… It’s not academic precision for novel molecules, but I hope it’s useful for your studying or general use!
Download 3D molecule models as OBJ, GLB or SDF
If you want to use your molecule drawing outside of this page, you can export the molecular model as a 3D object (.obj or .glb). Pro tip: You can import these into PowerPoint and get some nice animations and rotations / movements. I’m personally a sucker for the Morph transition – if you know, you know 😎. Here is an example of what this can look like.
You can also save export the molecule drawing as a SDF file, and use it for Chem3D or other applications.
If there are any bugs or you have suggestions, let me know!