GEMMI - library for structural biology

Gemmi is a library, accompanied by a set of programs, developed primarily for use in macromolecular crystallography (MX). For working with:

  • macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),

  • refinement restraints (CIF files) and small molecule models,

  • reflection data (MTZ and mmCIF formats),

  • crystallographic symmetry,

  • data on a 3D grid with crystallographic symmetry (electron density maps, masks, MRC/CCP4 format)

Parts of this library can be useful in structural bioinformatics (for symmetry-aware analysis of protein models), in chemical crystallography and in other molecular-structure sciences that use CIF files (we have the fastest open-source CIF parser).

Gemmi is open-source (MPL) and portable – it runs on Linux, Windows, MacOS and even inside a web browser if compiled to WebAssembly (here and here). It is written in C++14, with Python (3.8+) bindings, and with partial C and Fortran 2003 interface.

Occasionally, the project gets sidetracked into visualization of the PDB data.

Gemmi is a joint project of Global Phasing Ltd and CCP4. It is named after Gemmi Pass. The name can also be expanded as GEneral MacroMolecular I/o.

Source code repository: https://github.com/project-gemmi/gemmi

Note

You can ask questions in Discussions or Issues on GitHub. Alternatively, send me an email.

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