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.