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Avogadro alternatives: 2 apps ranked by verified data

Facts checked Nov 1, 2026AppBreakup editorialHow we rank

Common reasons people leave Avogadro: less suited to large proteins and cryo-EM maps, and no web or mobile version. We ranked 2 alternatives by how directly each one replaces Avogadro, then by reviews, real visits and how recently each app's facts were checked against its own website. Jmol currently ranks first.

Quick comparison

#AppPricingOpen sourcePlatformsVerified factsScore
1Jmol logoJmolOpen sourceYesWindows, macOS, Linux +14 of 454.5
  1. Jmol logo

    1. JmolTop pick

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

    Open sourceWindows, macOS, Linux, Web

    54.5

    score / 100

    Why switch from Avogadro

    A free viewer that also runs in web pages, for sharing structures online.

    Pros

    • 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

    Cons

    • Desktop app needs Java installed
    • Dated look compared with PyMOL or ChimeraX
    • Not built for cryo-EM maps or very large trajectories
    Visit Jmol Details and reviews
    How this score is calculated
    Editorial fit ×0.360
    Reviews ×0.363
    Clicks (90 days) ×0.150
    Freshness ×0.1585
    Votes ×0.150

    0 counted reviews, 0 up and 0 down votes. Full formula

    Is Jmol a good Avogadro alternative?

    Verified facts

    4 of 4 verified
    License
    GNU LGPL
    Checked Nov 1, 2026jmol.sourceforge.net(opens source in a new tab)
    Platforms
    Windows, macOS, Linux
    Checked Nov 1, 2026jmol.sourceforge.net(opens source in a new tab)
    Web version
    JSmol, no Java needed
    Checked Nov 1, 2026jmol.sourceforge.net(opens source in a new tab)
    Requirements
    Desktop app needs Java
    Checked Nov 1, 2026jmol.sourceforge.net(opens source in a new tab)

The best Avogadro alternative for…

The highest-ranked app in this list for each need.

Jmol logo

Best Avogadro alternative for most people

Jmol

A free viewer that also runs in web pages, for sharing structures online.

Jmol logo

Best Avogadro alternative for a free option

Jmol

A free viewer that also runs in web pages, for sharing structures online.

Jmol logo

Best Avogadro alternative for open source

Jmol

A free viewer that also runs in web pages, for sharing structures online.

PyMOL logo

Best Avogadro alternative for Mac

PyMOL

Higher-quality rendered figures of biomolecules, with Python scripting.

Jmol logo

Best Avogadro alternative for Windows

Jmol

A free viewer that also runs in web pages, for sharing structures online.

Jmol logo

Best Avogadro alternative for Linux

Jmol

A free viewer that also runs in web pages, for sharing structures online.

Jmol logo

Best Avogadro alternative for working in the browser

Jmol

A free viewer that also runs in web pages, for sharing structures online.

Avogadro alternatives: common questions

What is the best alternative to Avogadro?

Jmol ranks first right now. A free viewer that also runs in web pages, for sharing structures online.

Is there a free alternative to Avogadro?

Yes. Jmol (open source) has a free option. Check each app's verified facts for current plan limits.

Is there an open-source alternative to Avogadro?

Yes: Jmol.

Which Avogadro alternatives work on Linux?

Jmol and PyMOL run on Linux.

Why do people switch from Avogadro?

The complaints we hear most: less suited to large proteins and cryo-EM maps; no web or mobile version; windows on ARM is not supported yet.

How is this list ranked?

Every app is scored with the same published formula: how directly it replaces Avogadro, reviews (weighted by verification), visits from AppBreakup, how recently its facts were checked against its own website, and reader votes.