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Jmol

Free, open-source viewer for 3D chemical structures, on the desktop or in web pages.

Open sourceMolecular visualization software
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About Jmol

Jmol is an open-source viewer for chemical structures in 3D, covering small molecules, crystals, materials and biomolecules. It comes in two forms: a standalone Java desktop application, and JSmol, an HTML5/JavaScript version that runs in any modern browser without Java and can be embedded in web pages. That makes it a common choice for teaching sites, online courseware and chemical databases. It reads a very wide range of file formats, from PDB, mmCIF and MOL to output from quantum chemistry packages, and can show orbitals, surfaces, vibrations, symmetry and unit cells. It is scriptable (and accepts RasMol/Chime-style commands) and exports images and 3D formats. Jmol is free under the LGPL and runs on Windows, macOS and Linux. It suits educators, students and chemists who want a free viewer or need structures on the web; it is less polished for publication figures than PyMOL and less suited to cryo-EM work than ChimeraX.

Best for: Teachers, students and web developers who need a free structure viewer.

Pros and cons

What works

  • Free and open source under the LGPL
  • JSmol embeds interactive 3D structures in web pages without Java
  • Reads a very wide range of chemistry file formats
  • Translated into many languages

Why people leave

  • Desktop app needs Java installed
  • Dated look compared with PyMOL or ChimeraX
  • Not built for cryo-EM maps or very large trajectories

Top Jmol alternatives

See all 4
  1. 1PyMOL logo
    PyMOL

    More polished rendering for publication figures, with Python scripting.

    66.5
  2. 2Uc
    UCSF ChimeraX

    Modern free-for-academics tool with cryo-EM map support and VR.

    62.6
  3. 3VMD logo
    VMD

    Better for large biomolecular systems and simulation trajectories.

    59.6
  4. 4Avogadro logo
    Avogadro

    Free and open source like Jmol, but also lets you build and optimise molecules, not just view them.

    50.3

Why people left Jmol

In reviewers' own words, from reviews of the apps they moved to. These are their opinions, not ours.

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Reviews

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Jmol: common questions

Is Jmol free?

Yes. Jmol is free, open-source software.

Is Jmol open source?

Yes.

What platforms does Jmol run on?

Jmol is available for Windows, macOS, Linux and Web.

What are the best alternatives to Jmol?

The highest-ranked Jmol alternatives right now are PyMOL, UCSF ChimeraX and VMD. See the full ranked list for pricing, platforms and verified facts.

See all 4 Jmol alternatives