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Coot vs PyMOL: catalog facts
Coot	PyMOL
Best for: Structural biologists building and validating protein models	Best for: Researchers and students who visualize protein and molecular structures
Free Free and open source under GPL and LGPL licences.	Free + paid options The open-source build is free; Schrödinger's PyMOL bundles require a purchased license.
macOS, Linux	Windows, macOS, Linux
Broad set of model building and refinement tools Works with both X-ray and cryo-EM data All 3 strengths for Coot Broad set of model building and refinement tools Works with both X-ray and cryo-EM data Available through Debian, Ubuntu and Homebrew packages	Long-established molecular visualization tool Raytraced rendering of molecular structures All 4 strengths for PyMOL Long-established molecular visualization tool Raytraced rendering of molecular structures Open-source core with a permissive license Builds for Windows, macOS and Linux plus a conda channel
Prebuilt binaries for the 1.x series cover few platforms Specialist tool that assumes crystallography knowledge	Official installer bundles need a paid license Aimed at scientific users rather than casual learners
Downloadable app	Downloadable app
Open source	Open source
License: GPL-2.0-or-later, GPL-3.0-or-later and LGPL-3.0-or-later	License: Python-2.0
No account needed	No account needed
Offline features available	Offline features available
Official website Full listing and sources Sources for Coot www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot Catalog checked October 1, 2026	Official website Full listing and sources Sources for PyMOL pymol.org Catalog checked October 1, 2026

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