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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 CCPEM / 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:
Bugs and feedback please contact Tom Burnley / Colin Palmer at:
CCP-EM_beta Linux (updated 19/02/18)
CCP-EM_beta Linux (previous version, updated 01/11/17)
CCP-EM_beta Mac (updated 27/02/18)
XQuartz is required for Mac install
FlexEM and some other programs require Modeller to be installed and for users to have obtained a valid license key. Please register for a Modeller license key (free for acedemic use).
Linux: After running ./CCPEM-BINARY.setup you will be prompted to run ./Modeller.setup. Please run this and enter the license key when prompted.
Mac: Please download and install the Modeller Mac package and use default installation location.
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: 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 (Janelia Research Campus)
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)
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