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brew

Install gemmi with Homebrew, apt, MacPorts, Nix

Macromolecular crystallography library and utilities. Version 0.7.5 via Homebrew; verified 2026-06-21.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install gemmi

local Homebrew formula metadata

MacPortsverified · 94%
sudo port install gemmi

MacPorts ports tree · science/gemmi/Portfile · source: api.github.com

Linux

Debian aptverified · 92%
sudo apt install gemmi

Debian stable package indexes · gemmi · source: deb.debian.org

Nixverified · 92%
nix profile install nixpkgs#gemmi

nixpkgs package indexes · pkgs/by-name/ge/gemmi/package.nix · source: api.github.com

overview

Package summary

Macromolecular crystallography library and utilities

Commands and aliases

  • gemmi

history

Project history and usage

Gemmi is a C++ library and command-line toolkit for structural biology, especially macromolecular crystallography. It handles mmCIF, PDB, MTZ, CCP4/MRC maps, crystallographic symmetry, reflection data, and related file formats, with Python bindings and additional interfaces around the same core library.

Project history

Gemmi's repository begins in 2017 and its documentation identifies it as a joint project of Global Phasing Ltd and CCP4. The project name is both a reference to Gemmi Pass and an expansion of General MacroMolecular I/O, reflecting its emphasis on file formats and data structures used by crystallographers.

The project matured from a parser and utility collection into a broad structural-biology library. Its README and documentation describe C++14 code, Python bindings, a developing Fortran interface, partial WebAssembly bindings, web tools, and the `gemmi` command with many subcommands for validation, conversion, map handling, reflection data, and model analysis.

In 2022, Gemmi was published in the Journal of Open Source Software as 'GEMMI: A library for structural biology,' giving the project a citable software reference for scientific users.

Adoption history

Gemmi's adoption is anchored in crystallography infrastructure. The README names CCP4 and Global Phasing as institutional homes, while the JOSS paper and project documentation frame it as reusable infrastructure for programs that need fast, standards-aware handling of CIF-family files, structural models, maps, and reflection data.

Package availability in Homebrew, Debian, Ubuntu, MacPorts, and Nix makes Gemmi accessible outside specialist crystallography distributions, which matters for reproducible pipelines and notebooks that mix command-line conversion with Python analysis.

How it is used

Practitioners use Gemmi as a library when writing structural-biology software and as a CLI when inspecting, validating, converting, or extracting data from coordinate, CIF, MTZ, and CCP4/MRC files. The `gemmi` program includes subcommands such as `validate`, `grep`, `convert`, `cif2mtz`, `mtz2cif`, `map`, `sfcalc`, and `xds2mtz`.

Python users use the bindings for scripting and data analysis, while package maintainers care about the shared C++ core because it supports both standalone utilities and embedded scientific workflows.

Why package nerds care

Gemmi is package-nerd interesting because it turns hard scientific file-format support into one installable toolkit. It is small compared with full crystallography suites but intersects with many of them, so it often appears in environments where users need command-line conversion, Python bindings, and citation-grade provenance.

Timeline

  • 2017: Initial public repository commits.
  • 2018: Early 0.1.x releases appear.
  • 2022-05-04: Gemmi is published in the Journal of Open Source Software.
  • 2020s: Documentation expands around the `gemmi` command, Python API, C++ API, WebAssembly tools, and structural-biology workflows.

Related projects

  • Gemmi is related to CCP4, Global Phasing software, wwPDB/mmCIF tooling, MTZ and CCP4/MRC map workflows, GemmiMOL, and scientific Python pipelines for structural biology.

security posture

Risk level: green

library-like package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

  • library-like package without higher-risk signals

Signals

  • metadata:library-like

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Build metadata lists 1 build dependencies.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

CommandKindExposureNote
gemmicliglobal executable

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-07-08
manager version0.7.5
manager updated2026-06-21
local dataok
upstreamcurrent
latest detectedv0.7.5

https://github.com/project-gemmi/gemmi

  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:gemmi
Version0.7.5
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/gemmi
Homepagehttps://project-gemmi.github.io/
Repositoryhttps://github.com/project-gemmi/gemmi
Upstream docshttps://gemmi.readthedocs.io/
LicenseMPL-2.0
Source archivehttps://github.com/project-gemmi/gemmi/archive/refs/tags/v0.7.5.tar.gz
Last updated2026-06-21T00:20:16Z
Pulseupdated
Build dependenciescmake
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namegemmi
Version Scheme0
Revision0
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • stable

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

Debian apt95%

gemmi 0.6.5+ds-3

library for structural biology - executable

https://project-gemmi.github.io

sudo apt install gemmi
  • Section: science
  • Architecture: amd64
  • 4 dependencies
  • normalized package name match
  • Matched by: Gemmi
Debian stable package indexes · deb.debian.org · Debian stable package indexes: gemmi from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

gemmi-dev 0.6.5+ds-3

library for structural biology

https://project-gemmi.github.io

sudo apt install gemmi-dev
  • Section: libdevel
  • Architecture: amd64
  • Source Package: gemmi
  • 1 dependencies
  • normalized package name match
  • Matched by: Gemmi
Debian stable package indexes · deb.debian.org · Debian stable package indexes: gemmi-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

python3-gemmi 0.6.5+ds-3

library for structural biology - Python module

https://project-gemmi.github.io

sudo apt install python3-gemmi
  • Section: python
  • Architecture: amd64
  • Source Package: gemmi
  • 5 dependencies
  • normalized package name match
  • Matched by: Gemmi
Debian stable package indexes · deb.debian.org · Debian stable package indexes: python3-gemmi from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

gemmi

nix profile install nixpkgs#gemmi
  • normalized package name match
  • Matched by: Gemmi
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/ge/gemmi/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
Ubuntu apt95%

gemmi 0.6.4+ds-1build1

library for structural biology - executable

https://project-gemmi.github.io

sudo apt install gemmi
  • Section: universe/science
  • Architecture: amd64
  • 4 dependencies
  • normalized package name match
  • Matched by: Gemmi
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: gemmi from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

gemmi-dev 0.6.4+ds-1build1

library for structural biology

https://project-gemmi.github.io

sudo apt install gemmi-dev
  • Section: universe/libdevel
  • Architecture: amd64
  • Source Package: gemmi
  • normalized package name match
  • Matched by: Gemmi
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: gemmi-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

python3-gemmi 0.6.4+ds-1build1

library for structural biology - Python module

https://project-gemmi.github.io

sudo apt install python3-gemmi
  • Section: universe/python
  • Architecture: amd64
  • Source Package: gemmi
  • 5 dependencies
  • normalized package name match
  • Matched by: Gemmi
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: python3-gemmi from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
MacPorts95%

gemmi

sudo port install gemmi
  • normalized package name match
  • Matched by: Gemmi
MacPorts ports tree · api.github.com · MacPorts ports tree: science/gemmi/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • cmakeBuild dependency declared by Homebrew.

Same workflow

  • biosigShares av.db curated category or tags: c-plus-plus, cli, science.
  • ccfitsShares av.db curated category or tags: c-plus-plus, cli, science.
  • clhepShares av.db curated category or tags: c-plus-plus, cli, science.
  • clpShares av.db curated category or tags: c-plus-plus, cli, science.
  • dcmtkShares av.db curated category or tags: c-plus-plus, cli, science.
  • freelingShares av.db curated category or tags: c-plus-plus, cli, science.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Used sources

  • Geiger risk classifier
  • Nucleus package database
  • av.db category and tag curation
  • cross-ecosystem install command graph
  • curated package history
  • external package-manager database matches
  • package relationship graph
  • package version freshness
  • package-page enrichment