2dx is an initiative that aims at facilitating computer image processing in electron crystallography.
The 3D-FSC provides a quantitative measure of directional resolution anisotropy, which is caused by preferential orientation at the air-water interface, as described in Tan et al 2017.
APBS & PDB2PQR
APBS (Adaptive Poisson-Boltzmann Solver) and PDB2PQR are software packages designed to help you analyze the solvation properties of small and macro-molecules such as proteins, nucleic acids, and other complex systems.
Bsoft is a collection of programs and a platform for development of software for image processing in structural biology.
CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.
cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. It was developed by Tim Grant, Alexis Rohou and Nikolaus Grigorieff and comprises a number of tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions.
Computational Crystallography Toolbox (cctbx)
The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the PHENIX system.
CryoSPARC™ is an easy to use software tool that enables rapid, unbiased structure discovery of proteins and molecular complexes from cryo-EM data.
CTFFIND3 and CTFTILT are two programs for finding CTFs of electron micrographs.
EMAN2 is a scientific image processing suite with a primary focus on processing TEM image data. It provides various tools useful in structure determination for cryo-EM.
EMBuilder is a model building program for cryo-EM density maps. It is based on template matching method which is widely used in Crystallography. The suitable resolution for input map is higher than 3.5 Å.
This is the set of scripts used for the EMRinger paper (citation below). For the most up-to-date version of EMRinger, please use phenix.emringer or the integrated GUI version of EMRinger in the latest phenix nightly.
Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.
Gautomatch & Gctf
The programs of automated particle picking and CTF estimation that utilizes the GPU resources.
The Image Processing Library & Toolbox is an open-source project, released under the GNU General Public License. It is primarily aimed at the electron microscopy community, with particular emphasis on 2D electron crystallography.
Open-Source Computational Structural Biology Framework.
Oxford Particle Imaging Centre
Repository for Scipion, the scripts for local reconstruction, wrapped Python scripts for Relion, and so forth.
PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in cryo-EM.
Rosetta is a comprehensive software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. (Rosetta Commons; https://www.rosettacommons.org)
SerialEM is a program that can acquire a variety of data from electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods.
SPIDER & WEB
SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy.
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data.
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.
The Hitchhiker’s Guide to Python
This opinionated guide exists to provide both novice and expert Python developers a best practice handbook to the installation, configuration, and usage of Python on a daily basis.
PyCUDA lets you access Nvidia‘s CUDA parallel computation API from Python.
PyQtGraph is a pure-python graphics and GUI library built on PyQt4, PySide and numpy. It is intended for use in mathematics, scientific, engineering applications. Despite being written entirely in python, the library is very fast due to its heavy leverage of numpy for number crunching and Qt’s GraphicsView framework for fast display.