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PyMOL alternatives: 4 apps ranked by verified data

Facts checked Nov 1, 2026AppBreakup editorialHow we rank

Common reasons people leave PyMOL: official builds and support require a paid licence for research use, and educational builds can't be used for academic research or publication. We ranked 4 alternatives by how directly each one replaces PyMOL, then by reviews, real visits and how recently each app's facts were checked against its own website. UCSF ChimeraX currently ranks first.

Quick comparison

#AppPricingOpen sourcePlatformsVerified factsScore
1Jmol logoJmolOpen sourceYesWindows, macOS, Linux +14 of 459.6
  1. Jmol logo

    1. JmolTop pick

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

    Open sourceWindows, macOS, Linux, Web

    59.6

    score / 100

    Why switch from PyMOL

    Free, open-source viewer that also runs in web pages, good for teaching.

    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 ×0.377
    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 Jmol a good PyMOL 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 PyMOL alternative for…

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

Uc

Best PyMOL alternative for most people

UCSF ChimeraX

Free for academic and personal use, with strong cryo-EM map tools and VR support.

VMD logo

Best PyMOL alternative for a free option

VMD

Free viewer built for large systems and molecular dynamics trajectories.

Uc

Best PyMOL alternative for a free plan you can upgrade

UCSF ChimeraX

Free for academic and personal use, with strong cryo-EM map tools and VR support.

Jmol logo

Best PyMOL alternative for open source

Jmol

Free, open-source viewer that also runs in web pages, good for teaching.

Avogadro logo

Best PyMOL alternative for Mac

Avogadro

Free, open source and better suited to building and editing small molecules.

Uc

Best PyMOL alternative for Windows

UCSF ChimeraX

Free for academic and personal use, with strong cryo-EM map tools and VR support.

Uc

Best PyMOL alternative for Linux

UCSF ChimeraX

Free for academic and personal use, with strong cryo-EM map tools and VR support.

Jmol logo

Best PyMOL alternative for working in the browser

Jmol

Free, open-source viewer that also runs in web pages, good for teaching.

PyMOL alternatives: common questions

What is the best alternative to PyMOL?

UCSF ChimeraX ranks first right now. Free for academic and personal use, with strong cryo-EM map tools and VR support. VMD and Jmol follow it in our ranking.

Is there a free alternative to PyMOL?

Yes. UCSF ChimeraX (free plan + paid), VMD (free), Jmol (open source) 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 PyMOL?

Yes: Jmol.

Which PyMOL alternatives work on Linux?

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

Why do people switch from PyMOL?

The complaints we hear most: official builds and support require a paid licence for research use; educational builds can't be used for academic research or publication; weaker than ChimeraX for cryo-EM density maps and VR.

How is this list ranked?

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