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A free alternative to ChemDraw for chemistry figures
BioDiorama is a free, browser-based tool for chemistry figures. Type a compound name and it draws the skeletal formula from PubChem’s own structure data, or brings the molecule in as a 3D model you can style as spheres, sticks, surface or wireframe; it has more than 2,200 chemistry models — every element as an atom, orbitals, VSEPR shapes, crystals, ions and 1,600 real compounds — and it opens SMILES, MOL, SDF, MOL2, XYZ, mmCIF, PDB and PDBQT files from PyMOL, ChimeraX, AutoDock and Open Babel. It is not a structure editor: you do not draw a brand-new molecule bond by bond, you bring it in and style it.
Open BioDiorama See the 27,200 models
At a glance
| BioDiorama | ChemDraw | |
|---|---|---|
| What it costs | Free, with no account. | A paid licence, often through an institution. |
| Where it runs | In the browser. | Installed, with a cloud version. |
| Known compounds | By name, from PubChem: skeletal formula, 3D structure or crystal. | By name, from its own database and name-to-structure. |
| Drawing a new structure | Not bond by bond — bring it in as SMILES, MOL, SDF or MOL2 and restyle it. | Its core strength: a full structure editor. |
| 3D | A real 3D studio: molecules, orbitals, crystals, proteins and nanoparticles, lit and posed in a scene. | Chem3D for modelling and calculation. |
| Chemical intelligence | None — it draws, it does not check or calculate. | Name-to-structure, structure-to-name, NMR prediction, stoichiometry, property calculation. |
| Around the molecule | Cells, organs, lab equipment, animals and the rest of a 27,200-model biology library for the figure the molecule sits in. | Chemistry drawing objects. |
| Export | Editable PowerPoint (.pptx), layered SVG, 3D models (.glb), PDF, and TIFF or PNG up to 600 dpi. | CDX, CDXML, and the formats journals and ACS templates expect. |
What you get by switching
- A drug, metabolite, lipid or dye by name, as a skeletal formula or a 3D model, without a licence.
- The chemistry can sit inside the biology: a molecule binding a real PDB receptor, a nanoparticle in a cell, a reaction on a lab bench.
- Structures from the tools you already use — PyMOL, ChimeraX, AutoDock, Open Babel and Gypsum-DL files all open directly.
- Every element as an atom, orbitals, VSEPR shapes, crystals, ions and electrochemistry, for teaching figures.
- 600 dpi TIFF and vector SVG, so the figure meets a journal’s specification.
- PubChem data is public domain and PDB structures are CC0, so nothing in the way of publishing.
Where ChemDraw is still the better tool
Said plainly, because picking the wrong tool wastes more time than any figure saves.
- ChemDraw is a structure editor; BioDiorama is not. A novel structure has to be drawn elsewhere and brought in as SMILES or a MOL file.
- No name-to-structure for unpublished compounds, no structure-to-name, no NMR or property prediction, no stoichiometry.
- No reaction schemes with mechanism arrows drawn to chemical rules.
- No CDX or CDXML, and no ACS journal drawing templates.
Moving a figure across
- Open biodiorama.com and go to the 3D Studio.
- Type the compound name in the Library search, or paste a SMILES string, or drop in a MOL, SDF, MOL2, XYZ, mmCIF or PDB file.
- Choose how it is drawn — skeletal formula, spheres, sticks, surface, wireframe or crystal — and recolour the atoms and bonds.
- Add the context the figure needs: a receptor, a membrane, a cell, a piece of equipment.
- Export TIFF or PNG at 600 dpi for the journal, or SVG to keep it vector.
Questions people ask
Is there a free alternative to ChemDraw?
For drawing new structures, the usual free options are structure editors such as MarvinJS, ChemSketch or RDKit-based tools. For making the figure — a known compound drawn properly, in 3D or as a skeletal formula, inside a biological scene — BioDiorama is free and runs in the browser.
Can BioDiorama draw a skeletal formula?
Yes, for any compound PubChem knows: it uses PubChem’s own 2D layout, and you can recolour bonds and atoms.
Can I draw my own molecule in BioDiorama?
Not bond by bond. Paste a SMILES string or open a MOL, SDF, MOL2 or XYZ file and it comes in as a model you can restyle.
Can I show a drug bound to its protein target?
Yes. Load the protein from the Protein Data Bank or AlphaFold and the molecule from PubChem, and pose them together in the 3D Studio.
Will a chemistry journal accept these figures?
The export formats and resolutions are the ones journals ask for — 600 dpi TIFF, PDF and vector SVG. PubChem data is public domain and PDB structures are CC0, so there is nothing to clear.
Is BioDiorama affiliated with ChemDraw or Revvity?
No. ChemDraw is a trademark of its owner and is named here only for comparison.
Other comparisons
ChemDraw is a trademark of its owner. BioDiorama is an independent project, is not affiliated with or endorsed by it, and nothing here is a quotation of its terms: plans, prices and features change, so check ChemDraw’s own site before you decide.