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Jmol alternatives: 4 apps ranked by verified data

Facts checked Nov 1, 2026AppBreakup editorialHow we rank

Common reasons people leave Jmol: desktop app needs Java installed, and dated look compared with PyMOL or ChimeraX. We ranked 4 alternatives by how directly each one replaces Jmol, then by reviews, real visits and how recently each app's facts were checked against its own website. PyMOL currently ranks first.

Quick comparison

#AppPricingOpen sourcePlatformsVerified factsScore
1UcUCSF ChimeraXFree plan + paidNoWindows, macOS, Linux4 of 462.6
2VMD logoVMDFreeNoWindows, macOS, Linux4 of 459.6
3Avogadro logoAvogadroOpen sourceNoWindows, macOS, Linux5 of 550.3
  1. Uc

    1. UCSF ChimeraXTop pick

    Best for: Structural biologists working with cryo-EM maps, AlphaFold models and figures

    Free plan + paidWindows, macOS, Linux

    62.6

    score / 100

    Why switch from Jmol

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

    Pros

    • Free for academic, government, nonprofit and personal use
    • Strong tools for density maps, model fitting and segmentation
    • VR headset support, including shared multi-person sessions
    • Plugin Toolshed and Python scripting

    Cons

    • Commercial users must buy a licence
    • Not open source under an OSI licence
    • Less suited than VMD to analysing long simulation trajectories
    Visit UCSF ChimeraX Details and reviews
    How this score is calculated
    Editorial fit ×0.387
    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 UCSF ChimeraX a good Jmol alternative?

    Verified facts

    4 of 4 verified
    Free use
    Academic, government, nonprofit, personal
    Checked Oct 30, 2026cgl.ucsf.edu(opens source in a new tab)
    Commercial use
    Requires a commercial licence
    Checked Oct 30, 2026cgl.ucsf.edu(opens source in a new tab)
    VR support
    Quest, Valve Index, HTC Vive and others
    Checked Oct 30, 2026cgl.ucsf.edu(opens source in a new tab)
    Developer
    RBVI, UC San Francisco
    Checked Oct 30, 2026cgl.ucsf.edu(opens source in a new tab)
  2. VMD logo

    2. VMD

    Best for: Simulation researchers analysing molecular dynamics trajectories

    FreeWindows, macOS, Linux

    59.6

    score / 100

    Why switch from Jmol

    Better for large biomolecular systems and simulation trajectories.

    Pros

    • Free download with source code included
    • Handles very large systems and long trajectories
    • Large plugin library and Tcl/Python scripting
    • Pairs closely with the NAMD simulation engine

    Cons

    • Dated interface with a steep learning curve
    • Licence restricts commercial use and redistribution
    • Stable releases come out infrequently
    Visit VMD Details and reviews
    How this score is calculated
    Editorial fit ×0.377
    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 VMD a good Jmol alternative?

    Verified facts

    4 of 4 verified
    Price
    Free, includes source code
    Checked Nov 1, 2026ks.uiuc.edu(opens source in a new tab)
    Platforms
    macOS, Unix/Linux, Windows
    Checked Nov 1, 2026ks.uiuc.edu(opens source in a new tab)
    License
    Academic, research and internal business use
    Checked Nov 1, 2026ks.uiuc.edu(opens source in a new tab)
    Commercial use
    Requires a commercial licence
    Checked Nov 1, 2026ks.uiuc.edu(opens source in a new tab)
  3. Avogadro logo

    3. Avogadro

    Best for: Chemistry students and computational chemists who build molecules and prepare calculation inputs

    Open sourceWindows, macOS, Linux

    50.3

    score / 100

    Why switch from Jmol

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

    Pros

    • Free and open source under the BSD 3-clause licence
    • Builds and optimises molecules, not just displays them
    • Reads output from GAMESS, Gaussian, ORCA, NWChem and others

    Cons

    • Less suited to large proteins and cryo-EM maps
    • No web or mobile version
    • Windows on ARM is not supported yet
    Visit Avogadro Details and reviews
    How this score is calculated
    Editorial fit ×0.346
    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 Avogadro a good Jmol alternative?

    Verified facts

    5 of 5 verified
    License
    BSD 3-clause
    Checked Oct 29, 2026avogadro.cc(opens source in a new tab)
    Platforms
    Windows, Linux, macOS
    Checked Oct 29, 2026avogadro.cc(opens source in a new tab)
    Plugins
    Python
    Checked Oct 29, 2026avogadro.cc(opens source in a new tab)
    Calculation output parsing
    GAMESS, Gaussian, ORCA and more
    Checked Oct 29, 2026avogadro.cc(opens source in a new tab)
    Latest version
    2.1
    Checked Oct 29, 2026avogadro.cc(opens source in a new tab)

The best Jmol alternative for…

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

PyMOL logo

Best Jmol alternative for most people

PyMOL

More polished rendering for publication figures, with Python scripting.

VMD logo

Best Jmol alternative for a free option

VMD

Better for large biomolecular systems and simulation trajectories.

Uc

Best Jmol alternative for a free plan you can upgrade

UCSF ChimeraX

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

Avogadro logo

Best Jmol alternative for Mac

Avogadro

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

PyMOL logo

Best Jmol alternative for Windows

PyMOL

More polished rendering for publication figures, with Python scripting.

PyMOL logo

Best Jmol alternative for Linux

PyMOL

More polished rendering for publication figures, with Python scripting.

Jmol alternatives: common questions

What is the best alternative to Jmol?

PyMOL ranks first right now. More polished rendering for publication figures, with Python scripting. UCSF ChimeraX and VMD follow it in our ranking.

Is there a free alternative to Jmol?

Yes. UCSF ChimeraX (free plan + paid), VMD (free) and Avogadro (open source) have a free option. Check each app's verified facts for current plan limits.

Is there an open-source alternative to Jmol?

None of the 4 alternatives in this list is open source.

Which Jmol alternatives work on Linux?

PyMOL, UCSF ChimeraX, VMD and Avogadro run on Linux.

Why do people switch from Jmol?

The complaints we hear most: desktop app needs Java installed; dated look compared with PyMOL or ChimeraX; not built for cryo-EM maps or very large trajectories.

How is this list ranked?

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