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),
  • reflection data (MTZ and mmCIF formats),
  • data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
  • crystallographic symmetry.

Parts of this library can be useful in structural bioinformatics (for symmetry-aware analysis of protein models), 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. It is written in C++11, with Python (2 and 3) 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.

The project 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

Important

As of 2020 the library is under intensive development and not everything is documented yet. Just ask questions.