PyMOL

Molecular visualization program from Schrödinger, widely used for protein structure figures.

Verified facts: 9 of 9
Alternatives ranked: 4
Approved reviews: 0
Visits sent from here: 0

About PyMOL

PyMOL is a desktop molecular viewer that has long been a standard for looking at protein and small-molecule structures and making publication figures. You load structures (for example from the Protein Data Bank), switch between cartoon, surface and stick representations, measure distances, align structures and render high-quality images and movies. It is scriptable in Python and through its own command language, which makes figures reproducible. Schrödinger maintains it as a commercial product on an open-source foundation: the official builds need a paid licence (with academic and commercial subscriptions), free educational-use builds are available to teachers and students for coursework, and most of the source code is published so people can build an open-source version themselves. It runs on Windows, macOS and Linux. It suits structural biologists, chemists and students who want polished images and a scriptable viewer; people who need cryo-EM map analysis or VR may prefer ChimeraX, and those working with long simulation trajectories often use VMD.

Best for: Structural biologists and chemists making publication-quality molecular figures.

What works

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

Why people leave

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

Top PyMOL alternatives

See all 4

1Uc
UCSF ChimeraX
Free for academic and personal use, with strong cryo-EM map tools and VR support.
66.5
2
VMD
Free viewer built for large systems and molecular dynamics trajectories.
62.6
3
Jmol
Free, open-source viewer that also runs in web pages, good for teaching.
59.6
4
Avogadro
Free, open source and better suited to building and editing small molecules.
50.3

Why people left PyMOL

In reviewers' own words, from reviews of the apps they moved to. These are their opinions, not ours.

No switching stories yet. If you moved away from PyMOL, review the app you switched to and tell us why.

Reviews

No approved reviews yet. How we verify reviewers

Write a review of PyMOL

PyMOL: common questions

Is PyMOL free?

No, PyMOL is a paid product. Starting price: $99 a year (academic single user) (checked on PyMOL's own site).

Is PyMOL open source?

No, PyMOL is not open source. Open-source alternatives include Jmol.

What platforms does PyMOL run on?

PyMOL is available for Windows, macOS and Linux.

What are the best alternatives to PyMOL?

The highest-ranked PyMOL alternatives right now are UCSF ChimeraX, VMD and Jmol. See the full ranked list for pricing, platforms and verified facts.

See all 4 PyMOL alternatives

PyMOL facts

9 of 9 verified

Developer: Schrödinger; Checked Oct 29, 2026pymol.org(opens source in a new tab); “maintained and distributed by Schrödinger .”
Open source: Most source code, permissive license; Checked Oct 29, 2026pymol.org(opens source in a new tab); “most of its source code freely available under a permissive license.”
Platforms: Windows, macOS, Linux; Checked Oct 29, 2026pymol.org(opens source in a new tab); “Windows EXE Installer Windows ZIP Archive macOS DMG (Apple Silicon) Linux TAR.BZ2 Archive Or install from the Schrodinger Anaconda Channel.”
Education builds: Free for teachers and students; Checked Oct 29, 2026pymol.org(opens source in a new tab); “available at no cost to teachers and high school and college students”
Latest version: PyMOL 3.1; Checked Oct 29, 2026pymol.org(opens source in a new tab); “Introducing PyMOL 3.1”
Starting price: $99 a year (academic single user); Checked Nov 1, 2026pymol.org(opens source in a new tab); “Academic/Non-Profit Purchasing Prices for academic and non-profit use. Professional usage may include use of PyMOL by commercial scientists in non-profit projects and publications outside the scope”
Commercial single-user plan: $1,050 a year (25 or fewer employees); Checked Nov 1, 2026pymol.org(opens source in a new tab); “License 1 Year Subscription 2 Year Subscription 3 Year Subscription PyMOL - Single User Eligibility: Organization contains 25 or fewer employees $1,050”
Government single-user plan: $315 a year; Checked Nov 1, 2026pymol.org(opens source in a new tab); “Government Purchasing Prices for government use. Professional usage may include use of PyMOL by commercial scientists in non-profit projects and publications outside the scope of their employment.”
Student discount: Free for full-time students and teachers; Checked Nov 1, 2026pymol.org(opens source in a new tab); “available at no cost to full-time students and educators teaching full-time students.”