Coot (Crystallographic Object-Oriented Toolkit)

Coot is a powerful macromolecular model-building tool for analysing X-ray data and models (i.e. proteins, ligands, RNA and DNA).

There are many tools for model manipulation and building, such as minimization, molecular superposition, fragment rotation/translations, rotamer-fitting, de novo building and refinement.

Coot is used by scientists using X-ray crystallography or cryo-EM for analysis of proteins, electron density maps, protein interactions and drug design.

This repo hosts the flatpak wrapper for Coot, available at Flathub.

Coot is under active development at the upstream repo by Dr. Paul Emsley.

Installation

There are two types of build for different purposes.

Stable build

This is the latest stable version. It is suitable for the most people for daily use.

flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
flatpak install flathub io.github.pemsley.coot
flatpak run io.github.pemsley.coot

Beta build

This isn’t meant to be the nightly build, but for the release that has some level of testing and is expected to mostly work and be usable to non-developer end-users.

flatpak remote-add --if-not-exists flathub-beta https://flathub.org/beta-repo/flathub-beta.flatpakrepo
flatpak install flathub-beta io.github.pemsley.coot
flatpak run io.github.pemsley.coot//beta

Building

At first, Install flatpak-builder using Flatpak.

flatpak install flathub org.flatpak.Builder

Then, clone this repo to build the app using flatpak-builder.

git clone https://github.com/flathub/io.github.pemsley.coot.git
cd io.github.pemsley.coot
flatpak run org.flatpak.Builder --force-clean --sandbox --user --install --install-deps-from=flathub --ccache --mirror-screenshots-url=https://dl.flathub.org/media/ --repo=repo builddir io.github.pemsley.coot.yaml

Finally, you can run the app for testing.

flatpak run io.github.pemsley.coot