PyMOL

PyMOL's support for Apple Silicon has evolved gradually. The open-source build became available for native M1/M2 installation via Homebrew around 2021–2022, and conda-forge has since added arm64 packages for the open-source version. However, as of mid-2026, Schrödinger's official proprietary PyMOL binaries — the most commonly used distribution — do not ship a native Apple Silicon build by default; the standard download from schrödinger.com remains Intel-only and runs under Rosetta. If you are using the Schrödinger proprietary version, the most straightforward path to native performance is to uninstall it and switch to the open-source PyMOL via Homebrew, which is mature, actively maintained, and runs natively on M-series Macs. Installation is simple: install Homebrew (brew.sh) if you don't have it, then run "brew install pymol". This will pull the native arm64 build and set it up automatically. Alternatively, if you use conda, the open-source pymol-open-source package on conda-forge now includes arm64 builds (though Schrödinger's own conda channel still does not). The open-source version lacks some of Schrödinger's proprietary extensions, but it handles structure visualization, analysis and publication graphics at a level suitable for most academic and research workflows. Given that Apple will remove Rosetta 2 in macOS 28 (September 2028), switching to a native-capable distribution now is important to avoid the app stopping completely at that time.