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

#	App	Pricing	Open source	Platforms	Verified facts	Score
1	Jmol	Open source	Yes	Windows, macOS, Linux +1	4 of 4	54.5
2	PyMOL	Paid	No	Windows, macOS, Linux	9 of 9	50.3

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)
2. PyMOL
Best for: Structural biologists and chemists making publication-quality molecular figures
PaidWindows, macOS, Linux
50.3
score / 100
Why switch from Avogadro
Higher-quality rendered figures of biomolecules, with Python scripting.
Pros
Excellent rendering for publication figures and movies
Scriptable with Python for reproducible work
Most source code is open, so a free open-source build exists
Free educational builds for students and teachers
Cons
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
Visit PyMOL 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 PyMOL a good Avogadro alternative?
Verified facts
9 of 9 verified
Developer
Schrödinger
Checked Oct 29, 2026pymol.org(opens source in a new tab)
Open source
Most source code, permissive license
Checked Oct 29, 2026pymol.org(opens source in a new tab)
Platforms
Windows, macOS, Linux
Checked Oct 29, 2026pymol.org(opens source in a new tab)
Education builds
Free for teachers and students
Checked Oct 29, 2026pymol.org(opens source in a new tab)
Latest version
PyMOL 3.1
Checked Oct 29, 2026pymol.org(opens source in a new tab)
Starting price
$99 a year (academic single user)
Checked Nov 1, 2026pymol.org(opens source in a new tab)
Commercial single-user plan
$1,050 a year (25 or fewer employees)
Checked Nov 1, 2026pymol.org(opens source in a new tab)
Government single-user plan
$315 a year
Checked Nov 1, 2026pymol.org(opens source in a new tab)
Student discount
Free for full-time students and teachers
Checked Nov 1, 2026pymol.org(opens source in a new tab)