# Install pymol with Homebrew, apt, dnf, MacPorts, Nix, pacman, winget, zypper Molecular visualization system. Version 3.1.0 via Homebrew; verified from local package data. ## Install ```sh sudo av install brew:pymol ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install pymol ``` Evidence: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install pymol ``` Evidence: MacPorts ports tree: science/pymol/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install pymol ``` Evidence: Debian stable package indexes: pymol from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - dnf (92%): ```sh sudo dnf install pymol ``` Evidence: Fedora Rawhide package metadata: pymol from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst - Nix (92%): ```sh nix profile install nixpkgs#pymol ``` Evidence: nixpkgs package indexes: pkgs/by-name/py/pymol/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - pacman (92%): ```sh sudo pacman -S pymol ``` Evidence: Arch Linux sync databases: pymol from https://geo.mirror.pkgbuild.com/extra/os/x86_64/extra.db.tar.gz - zypper (92%): ```sh sudo zypper install python311-pymol ``` Evidence: openSUSE Tumbleweed package metadata: python311-pymol from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst ### Windows - winget (92%): ```sh winget install --id Schrodinger.PyMOL -e ``` Evidence: Windows Package Manager source index: Schrodinger.PyMOL from https://cdn.winget.microsoft.com/cache/source.msix ## Package facts - **Package key:** brew:pymol - **Package manager:** Homebrew - **Package manager page:** - **Version:** 3.1.0 - **Source summary:** Molecular visualization system - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** LicenseRef-Homebrew-cannot-represent - **Source archive:** - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - pymol (cli) - pymol (alias) ## Dependencies - freetype - glew - libpng - netcdf - numpy - pyqt - python@3.14 ## Build dependencies - cmake - glm - msgpack-cxx - python-setuptools ## Uses from macOS - libxml2 ## Install behavior - Post-install hook: not defined - Caveats: To generate movies, run `brew install ffmpeg`. - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 3.1.0 - Local data: ok - Upstream repository: https://github.com/schrodinger/pymol-open-source - Upstream latest detected: v3.1.0 (current) - info: No package-manager update timestamp was available. ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Configuration and credential file locations These source-backed paths show where this package keeps local settings or durable credentials. Automic Vault can use them as review targets for secret scanning, migration, and command approval. ## Configuration files - Unix: ~/.pymolrc, ~/.pymolrc.py ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** pymol - **Version Scheme:** 0 - **Revision:** 3 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Other Package-Manager Records - Debian apt - pymol - 3.1.0+dfsg-1: normalized package name match | Debian stable package indexes: pymol from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Molecular Graphics System | https://www.pymol.org - Debian apt - pymol-data - 3.1.0+dfsg-1: normalized package name match | Debian stable package indexes: pymol-data from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | data files for PyMOL | https://www.pymol.org - Debian apt - python3-pymol - 3.1.0+dfsg-1: normalized package name match | Debian stable package indexes: python3-pymol from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Molecular Graphics System (Python 3 modules) | https://www.pymol.org - Nix - pymol: normalized package name match | nixpkgs package indexes: pkgs/by-name/py/pymol/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - pymol - 2.5.0+dfsg-1build6: normalized package name match | Ubuntu 24.04 LTS package indexes: pymol from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Molecular Graphics System | https://www.pymol.org - Ubuntu apt - pymol-data - 2.5.0+dfsg-1build6: normalized package name match | Ubuntu 24.04 LTS package indexes: pymol-data from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | data files for PyMOL | https://www.pymol.org - Ubuntu apt - python3-pymol - 2.5.0+dfsg-1build6: normalized package name match | Ubuntu 24.04 LTS package indexes: python3-pymol from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Molecular Graphics System (Python 3 modules) | https://www.pymol.org - dnf - pymol - 3.1.0-15.fc45: normalized package name match | Fedora Rawhide package metadata: pymol from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst | PyMOL Molecular Graphics System | http://www.pymol.org - dnf - pymol+tests - 3.1.0-15.fc45: normalized package name match | Fedora Rawhide package metadata: pymol+tests from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst | Metapackage for PyMOL: tests | http://www.pymol.org - pacman - pymol - 3.1.0-5: normalized package name match | Arch Linux sync databases: pymol from https://geo.mirror.pkgbuild.com/extra/os/x86_64/extra.db.tar.gz | Molecular visualization system on an Open Source foundation | https://pymol.org - zypper - python311-pymol - 3.1.0-4.3: normalized package name match | openSUSE Tumbleweed package metadata: python311-pymol from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst | A Molecular Viewer | https://pymol.org/ - zypper - python313-pymol - 3.1.0-4.3: normalized package name match | openSUSE Tumbleweed package metadata: python313-pymol from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst | A Molecular Viewer | https://pymol.org/ - zypper - python314-pymol - 3.1.0-4.3: normalized package name match | openSUSE Tumbleweed package metadata: python314-pymol from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst | A Molecular Viewer | https://pymol.org/ - MacPorts - pymol: normalized package name match | MacPorts ports tree: science/pymol/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 - winget - Schrodinger.PyMOL: normalized package name match | Windows Package Manager source index: Schrodinger.PyMOL from https://cdn.winget.microsoft.com/cache/source.msix ## Related links - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Media and graphics packages](https://www.automicvault.com/pkg/media-graphics-tools/) - Matched media, image, audio, video, or graphics metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [freetype](https://www.automicvault.com/pkg/brew/freetype/) - Runtime dependency declared by Homebrew. - [glew](https://www.automicvault.com/pkg/brew/glew/) - Runtime dependency declared by Homebrew. - [libpng](https://www.automicvault.com/pkg/brew/libpng/) - Runtime dependency declared by Homebrew. - [netcdf](https://www.automicvault.com/pkg/brew/netcdf/) - Runtime dependency declared by Homebrew. - [numpy](https://www.automicvault.com/pkg/brew/numpy/) - Runtime dependency declared by Homebrew. - [pyqt](https://www.automicvault.com/pkg/brew/pyqt/) - Runtime dependency declared by Homebrew. - [python@3.14](https://www.automicvault.com/pkg/brew/python-3-14/) - Runtime dependency declared by Homebrew. - [cmake](https://www.automicvault.com/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [freesasa](https://www.automicvault.com/pkg/brew/freesasa/) - Shares av.db curated category or tags: cli, science, structural-biology. - [gabedit](https://www.automicvault.com/pkg/brew/gabedit/) - Shares av.db curated category or tags: chemistry, cli, science. - [gemmi](https://www.automicvault.com/pkg/brew/gemmi/) - Shares av.db curated category or tags: cli, science, structural-biology. - [inchi](https://www.automicvault.com/pkg/brew/inchi/) - Shares av.db curated category or tags: chemistry, cli, science. - [open-babel](https://www.automicvault.com/pkg/brew/open-babel/) - Shares av.db curated category or tags: chemistry, cli, science. - [packmol](https://www.automicvault.com/pkg/brew/packmol/) - Shares av.db curated category or tags: chemistry, cli, science. - [vtk](https://www.automicvault.com/pkg/brew/vtk/) - Shares av.db curated category or tags: 3d-graphics, cli, science. - [aamath](https://www.automicvault.com/pkg/brew/aamath/) - Shares av.db curated category or tags: cli, science. - [opencv](https://www.automicvault.com/pkg/brew/opencv/) - Both packages touch the same language runtime or ecosystem. Shared terms: cli, freetype, glew, libpng, numpy. - [root](https://www.automicvault.com/pkg/brew/root/) - Both packages touch the same language runtime or ecosystem. Shared terms: cli, freetype, libpng, numpy, python. ## Combined YAML source View the package source record on GitHub. [combined/pymol.yml](https://github.com/automic-vault/db/blob/main/combined/pymol.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated configuration and credential file locations - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph