Coot Software Download

04-03-2021

Coot Software Download

CCP-EM software suite

Coot Software Download Version
Coot Windows
Coot Software Download Windows 10
Coot Software Download App

Latest releases

Stable

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CCP-EM v1.5.0 Linux (updated 29 Oct 2020)

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization.

CCP-EM v1.5.0 Mac (updated 29 Oct 2020)

Release notes. See below for installation instructions.

Nightly

Latest CCP-EM nightly for Linux (updated 4 Dec 2020)

Latest CCP-EM nightly for Mac (updated 5 Dec 2020)

Nightly builds have the latest features but also have a higher chance of bugs or errors.(If you find any bugs, please let us know!)Previous nightly releases and older stable versions can be found in thedownload directory.

Overview

The CCP-EM software suite is a package containing tools for cryo-EM, including:

Buccaneer & Nautilus

The suite is described in more detail in this article:

Recent developments in the CCP-EM software suite (T. Burnley, C.M. Palmer and M.D. Winn, Acta Cryst. D73, 469 - 477, 2017).

The CCP-EM suite is free of charge for non-profit use under theCCP-EM academic software licence.For-profit users should please contact ccpemlicensing@stfc.ac.ukfor information on commercial licencing. Further details are available on the licensing page.

For talks, tutorials and example data for our model building tools such as REFMAC, LocScale, Coot, Flex-EM, Buccaneer & Nautilus please see the Icknield workshop page.

To report bugs or give feedback please contact Tom Burnley / Colin Palmer at:ccpem@stfc.ac.uk

Installation

Download ccpem-<version>.tar.gz from the link above
tar -xzvf ccpem-<version>.tar.gz to unpack
cd ccpem-<version>
./install_ccpem.sh
source setup_ccpem.sh (or setup_ccpem.csh for csh)

CCP-EM contains RELION v3.0 and OpenMPI. If you have existing copies of these programs on your computer, please take care when setting up your shell environment to ensure you use the intended version. Also note that no programs are included for CTF estimation. To run this task from the RELION GUI, please install CTFFIND4 or Gctf separately.

Running

ccpem for main GUI
ccpem-<task name> for direct access to tasks (e.g. ccpem-refmac)
ccpem-python for CCP-EM Python environment
relion for RELION GUI

Known issues

There are some known problems running CCP-EM on certain operating systems. Please seethis page for details and possible solutions.

To run HARUSPEX, some additional software and configuration is needed. Instructions areavailable here.

Pre-requisites

CCP4

CCP-EM uses programs from CCP4 for a number of tasks. To use those tasks, please install CCP4 fromhttp://www.ccp4.ac.uk/download/ and activate itbefore running CCP-EM.

CCP-EM is developed using the latest update of CCP4. You can manage updates via the CCP4 update manager - run ccp4um.

Modeller

FlexEM and some other programs require Modeller to be installed and for users to have obtained a valid licence key. Please register for a Modeller licence key (free for academic use).

Linux:After running ./install_ccpem.sh you will be prompted to run ./install_modeller.sh. Please run this and enter the license key when prompted.

Mac:Please download and install the Modeller Mac package and use default installation location.