Collaborative Computational Project
for Electron cryo-Microscopy

MRC

CCP-EM downloads

CCP-EM beta release

CCP-EM intends to distribute a software suite containing tools for cryo-EM. At present, a beta-release is available for Linux64. This is available as part of the CCP4 nightly build, with which it shares a build system and some libraries and programs. In due course, a slimmer version will be available. Brief instructions:

  1. Download ccp4-linux64-latest.tar.bz2 from the link above
  2. tar xjf ccp4-linux64-latest.tar.bz2 to unpack
  3. cd ccp4-linux64-XXX
  4. ./BINARY.setup
  5. source bin/ccp4.setup-sh (or ccp4.setup-csh)
  6. From command line: "ccpem" for main GUI, "ccpem-refmac" for direct access to tasks, "ccpem-python" for Python access to CCP-EM modules
Note, you should hold a valid CCP4 licence. FlexEM requires Modeller to be installed, and ccpem-python edited to set the Modeller path. To do so edit ccp4-linux64-XXX/bin/ccpem-python to contain MODELLER="/usr/lib/python2.7/dist-packages/" or similar.

Refmac tools for EM

Refmac is a maximum likelihood structure refinement program, originally developed for X-ray crystallography (CCP4 required - ccp4.ac.uk).

Scripts are provided by Garib Murshudov (MRC-LMB) for changing the cell of PDB file, converting maps to structure factors (with blurring / sharpening), placing a PDB structure in a map, global refinement and local refinement. Instructions and example data are also provided.

Refmac_scripts (updated 8/3/16).

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.

README file for software
source code and test data v0.0.1
Linux binaries v0.0.1
Windows binaries v0.0.1

Johan Hattne, Tamir Gonen (Janelia Research Campus)
http://cryoem.janelia.org/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)

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