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CCP-EM software suite
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.
CCP-EM 20200116 Linux (updated 16 Jan 2020)
CCP-EM 20200115 Mac (updated 15 Jan 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 the download directory.
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 firstname.lastname@example.org 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@example.com
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.
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
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.
The latest version of XQuartz (2.7.11) is required for Mac install.
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.
MpUL-multi: Software for Calculation of Amyloid Fibril Mass per Unit Length
from TB-TEM Images.
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.
Johan Hattne, Tamir Gonen (UCLA)
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!
Software for 3D reconstruction of tip complexes - Ariel Blocker
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