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CCP-EM Doppio
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CCP-EM software suite v1The previous "version 1" CCP-EM software suite is still available, though it is no longer actively developed. We recommend you use the final builds: Last CCP-EM nightly for Linux (updated 8 Nov 2022) Last CCP-EM nightly for Mac (updated 8 Nov 2022) CCP-EM 20221108 includes RELION 4.0. It is the last version that will support Red Hat / CentOS 6 or similarly old Linux versions. The previous stable release version 1.6.0, along with previous nightly releases and older stable versions, can be found in the download directory. CCP-EM 1.6 was the last release that included RELION 3.1. 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
OverviewThe 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
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
Known issuesThere 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-requisitesCCP4
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
ModellerFlexEM 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. XQuartzXQuartz is required for CCP-EM on Macs. Please install seperately. We recommend XQuartz-2.8.2 however macOS 10.14 (Mojave) only works with XQuartz-2.8.0. This may apply to other older macOS versions. Operating systemsCCP-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
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 diffractionThe 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 DIALS 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) 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).
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Software for Particle Picking - Alan RosemanThe 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!
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Software for 3D reconstruction of tip complexes - Ariel BlockerThese 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).
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MRC Image Processing System - Tony Crowther, Richard Henderson & Jude Short (Smith)
A pre-compiled copy of the MRC image processing system (2010 version) is included in the CCP-EM suite. The source code for the stand-alone versions is also available here. Installation is described in the README file. First build all the libraries and executables using a .bld file specific to your system. Binaries will then be written to image2020/bin (or image2010/bin for the older version) and all have the extension .exe
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CCP-EM uses programs from CCP4 for a number of tasks. To use those tasks, please install CCP4 from
MpUL-multi: Software for Calculation of Amyloid Fibril Mass per Unit Length
from TB-TEM Images.