Collaborative Computational Project
for Electron cryo-Microscopy

MRC

CCP-EM downloads

CCP-EM software suite

Latest release

CCP-EM v1.4.1 Linux (updated 25 Nov 2019)

CCP-EM v1.4.1 Mac (updated 25 Nov 2019)

Release notes. See below for installation instructions.

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 ccpemlicensing@stfc.ac.uk 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: ccpem@stfc.ac.uk

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 v3.0 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

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 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.

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.

Other CCP-EM versions

Latest nightly releases

CCP-EM 20191105 Linux (updated 5 Nov 2019)

CCP-EM 20191105 Mac (updated 5 Nov 2019)

Previous nightly releases

CCP-EM 20191029 Linux (updated 29 Oct 2019)

CCP-EM 20191029 Mac (updated 29 Oct 2019)

CCP-EM 20190901 Linux (updated 1 Sep 2019)

CCP-EM 20190902 Mac (updated 2 Sep 2019)

Previous stable release

CCP-EM v1.3.0 Linux (updated 12 April 2019)

CCP-EM v1.3.0 Mac (updated 12 April 2019)

Release notes

MpUL-multi

MpUL-multi: Software for Calculation of Amyloid Fibril Mass per Unit Length from TB-TEM Images.
Matthew G. Iadanza, Matthew P. Jackson, Sheena E. Radford and Neil A. Ranson.
Astbury Centre for Structural Molecular Biology, Leeds, UK.

MpUL-multi is a program for calculating the mass per unit length (MPL) of amyloid fibrils from dark field imaging, by comparing to a standard of known MPL. A graphical user interface allows for simple designation of fibrils and standards. A second program averages intensities from multiple TMV molecules for accurate standard determination, makes multiple measurements along a given fibril, and calculates the MPL. The software is written in Python, and requires a local installation of FIJI or ImageJ. Download and unpack this file, and follow the instructions in README.txt.

A paper describing the approach has been submitted.

TVIPS tools for electron diffraction

The tiff2smv and tvips2smv utilities convert sequences of related electron diffraction images, or sweeps, recorded by Tietz Video and Image Processing Systems (TVIPS) cameras to the Super Marty View (SMV) format. Output SMV images are directly suitable for further processing in suites such as MOSFLM or XDS. tiff2smv supports TIFF images written by either EMMENU or EM_Player, as long as their pixel intensities can be losslessly represented as 16-bit unsigned integers. tvips2smv supports all TVIPS set files written by EMMENU.

Availability: The software is copyright Howard Hughes Medical Institute, and made available under a permissive Internet Software Consortium license.

Updated to version 0.0.3 (8/5/2018)
README file for software
source code and test data v0.0.3
Linux binaries v0.0.3
MacOS binaries v0.0.3
Windows binaries v0.0.3

Johan Hattne, Tamir Gonen (UCLA)
https://cryoem.ucla.edu/pages/MicroED

Shape Matching for Structural Biology (SMaSB)

The SMaSB software package has been developed to perform volume matching between a query volume and another volume or set of volumes. The primary aim is to search for similar volumes, rather than to optimise a particular fit. The software is primarily a set of Python codes, and has been extensively tested in Ubuntu 12.04 and Mac. More ...

SMaSB - download SMaSB (updated 24/5/16).

This software underpins the PDBeShape service. The authors are Agnel Praveen Joseph, Ingvar Lagerstedt, Ardan Patwardhan and Martyn Winn, with invaluable help from Irene Farabella and Maya Topf. Part of EU-funded BioMedBridges.

Software for Particle Picking - Alan Roseman

The following software is written by Alan Roseman's group at the University of Manchester, UK. The software is distributed under GPLv3. If you download/use the software, please send the author a quick email - improvements to the software depend on future funding which depends on measureable impact!

WeightedFLCF_lib.f90
Library of subroutines for implementation and Calculation of Weighted Fast Local Correlation Functions
FindEM2
Program for particle picking from electron micrographs.
FindEM2SK (FindEM2 Stacks Version)
Program to optimize particle selection and template based alignments, for single particle analysis TEM.
LinkEM
Package of programs and utilities to implement a method to analyse heterogeneity of a molecular population imaged in electron micrographs.

Software for 3D reconstruction of tip complexes - Ariel Blocker

These 2 packages are hosted by CCPEM on behalf of Ariel Blocker (Ariel.Blocker@bris.ac.uk), and are the data and scripts used in Cheung et al. (2014).

T3SS_TC 3D Reconstruction
Package of programs, instructions and test data (T3SS needle tips) to reconstruct in 3D an asymmetric complex at the tip of a filament of known helical symmetry.
GhostBuster
The GhostBuster procedure is a package of scripts, instructions, and test data (T3SS needle tips) that implements a method to improve the azimuthal alignment of particles derived from a 3D reconstruction from the T3SS reconstruction above (T3SS_TC 3D reconstruction).

MRC Image Processing System - Tony Crowther, Richard Henderson & Jude Short (Smith)

The MRC image processing system includes a number of image processing tools as well as the Ximdisp display program. An overview of the system is available on the MRC-LMB website.

A pre-compiled copy of the MRC image processing system is included in the CCP-EM suite. The source code for the stand-alone version is also available here.

Installation is described in /image2010/README. First build all the libraries and executables using a .bld file specific to your system. Binaries will then be written to /image2010/bin and all have the extension .exe

image2010.tar.gz