CCP-EM: Downloads

CCP-EM software suite

CCP-EM Doppio

The next generation of CCP-EM software, named Doppio, is now available in public beta release.
Doppio will grow to become a fully-featured new user interface for CCP-EM and RELION software.
This early beta version has some limitations, missing features and known problems but should
still be mostly stable and usable. If you find any unexpected bugs, please report them to the
CCP-EM team at [email protected].

Please start by reading the user guide and the
release notes.
Doppio downloads can be found here.

CCP-EM suite v1

Version 1 of the CCP-EM suite is still available. We recommend you use the most recent nightly builds:

Latest CCP-EM nightly for Linux (updated 8 Nov 2022)

Latest CCP-EM nightly for Mac (updated 8 Nov 2022)

The previous stable release version 1.6.0 is also still available:

CCP-EM v1.6.0 Linux (updated 8 Apr 2022)

CCP-EM v1.6.0 Mac (updated 8 Apr 2022)

Release notes. See below for installation instructions.

CCP-EM 1.6 is the last release that will include Python 2.7, Coot 0.9 and RELION 3.1. Future CCP-EM versions will use Python 3,
Coot 1 and RELION 4. It is also the last release that will support Red Hat / CentOS 6 or similarly old Linux versions.

As a convenience to Mac users, we have also produced a
standalone build of Coot v0.9.8.1 for Mac OS X. This was made using the normal CCP-EM build
system and it has not been tested thoroughly in this standalone form. It is possible there could be problems because the rest of
the CCP-EM suite is missing. To install, download the file, remove extended file attributes with
xattr -c coot-0.9.8.1-macosx-x86_64.tar.gz, unpack with tar -xzf coot-0.9.8.1-macosx-x86_64.tar.gz,
and then run coot-0.9.8.1/bin/coot (or put the coot-0.9.8.1/bin directory on your path and run
coot). If you do run into any problems, please let us know or use Coot from the
main CCP-EM suite package.

Previous nightly releases and stable versions can be found in the
download directory.

Overview

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

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 the
CCP-EM academic software licence.
For-profit users should please contact [email protected]
for 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:
[email protected]

Installation

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

CCP-EM contains RELION v3.1 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 see
this page for details and possible solutions.

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

Pre-requisites

CCP4

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

CCP-EM v1.6 has been checked for compatibility with CCP4 v7.1.018 and v8.0.010. In general we
recommend 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.

XQuartz

The latest version of XQuartz (2.7.11) is required for Mac install.

Operating systems

CCP-EM for Linux is built on Scientific Linux 6.10. We expect this to work on all Linux versions released since approximately 2010.
It is tested on Scientific Linux 6.10, Scientific Linux 7.5, Red Hat Enterprise Linux 6.10, Ubuntu 16.04 and Ubuntu 18.04.

CCP-EM for Mac is built on OS X 10.14 using the 10.9 SDK, and tested on OS X 10.11 and later.