PyMOL alternatives: 4 apps ranked by verified data
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.
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Show all 4 alternativesThe best PyMOL alternative for…
The highest-ranked app in this list for each need.
Best PyMOL alternative for most people
UCSF ChimeraXFree for academic and personal use, with strong cryo-EM map tools and VR support.
Best PyMOL alternative for a free option
VMDFree viewer built for large systems and molecular dynamics trajectories.
Best PyMOL alternative for a free plan you can upgrade
UCSF ChimeraXFree for academic and personal use, with strong cryo-EM map tools and VR support.
Best PyMOL alternative for open source
JmolFree, open-source viewer that also runs in web pages, good for teaching.
Best PyMOL alternative for Mac
AvogadroFree, open source and better suited to building and editing small molecules.
Best PyMOL alternative for Windows
UCSF ChimeraXFree for academic and personal use, with strong cryo-EM map tools and VR support.
Best PyMOL alternative for Linux
UCSF ChimeraXFree for academic and personal use, with strong cryo-EM map tools and VR support.
Best PyMOL alternative for working in the browser
JmolFree, 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.