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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
1UcUCSF ChimeraXFree plan + paidNoWindows, macOS, Linux4 of 466.5
2VMD logoVMDFreeNoWindows, macOS, Linux4 of 462.6
3Jmol logoJmolOpen sourceYesWindows, macOS, Linux +14 of 459.6
4Avogadro 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

    66.5

    score / 100

    Why switch from PyMOL

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

    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 ×0.3100
    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 PyMOL 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

    62.6

    score / 100

    Why switch from PyMOL

    Free viewer built for large systems and molecular dynamics 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 ×0.387
    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 VMD a good PyMOL 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. Jmol logo

    3. Jmol

    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)
  4. Avogadro logo

    4. 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 PyMOL

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

    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 PyMOL 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 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.