Cryo-EM learning center
For those willing to expand their knowledge in the field of (cryo)electron microscopy. The manufacturer of cryo-microscopes, Thermo Fisher Scientific, provides the Cryo-EM University e-learning platform. This resource hub contains rich and reliable technical content designed both for new and experienced researchers who are exploring the capabilities of cryo-EM.
Cryo-EM-University serves as an introduction to the field and is intended for participants of all levels. Upon course completion, you will gain a fundamental knowledge of cryo-EM, pick up tips and tricks for overcoming sample preparation challenges, and receive valuable practical advice on the cryo-EM workflow.
General information about the software platform for single particle analysis (SPA), cryo-electron tomography (cET) and microcrystal electron diffraction (MicroED) data analysis
cryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a software solution for complete processing of single-particle cryo-electron microscopy data. CryoSPARC is useful for solving cryo-EM structures of proteins, nucleic acids and whole viruses. The software allows to deal with flexible molecules, helical constructs, phase plate and negative stain data. CryoSPARC is developed and supported by Structura Biotechnology Inc. And is available free of charge for non-profit academic research.
Relion (for REgularised LIkelihood OptimisatioN) is a software package that employs an empirical Bayesian approach for electron cryo-microscopy structure determination. Platform is developed by the group of Sjors Scheres at the MRC Laboratory of Molecular Biology, Cambridge, UK.
Relion is distributed under a GPLv2 license, i.e. anyone (including commercial users) can download, use and modify Relion for free.
Relion is distributed under a GPLv2 license, i.e. anyone (including commercial users) can download, use and modify Relion for free.
Warp enables pre-processing and visualisation of cryo-microscopic images (SPA or tomographic tilt series). The software further includes deep-learning-based models for accurate particle picking and image denoising. The output from Warp can be used in established programs for particle classification and 3D-map refinement (CryoSPARC, Relion).
M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and improves the results of structure determination. M provides a unified optimization framework for both in vitro frame series and in situ tomographic tilt series data.
The software is developed and shared by Dimitry Tegunov & Patrick Cramer from Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and improves the results of structure determination. M provides a unified optimization framework for both in vitro frame series and in situ tomographic tilt series data.
The software is developed and shared by Dimitry Tegunov & Patrick Cramer from Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
EMAN2 (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs (3D volumetric models from 2D cryo-EM images). The suite also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2D crystallography and whole-cell tomography.
All EMAN2 programs, including GUI programs, are written in Python scripting language. The package is provided free of charge.
All EMAN2 programs, including GUI programs, are written in Python scripting language. The package is provided free of charge.
Software for visualization, analysis and presentation of 3D structure of molecules, most often applied using output from established programs for particle classification and 3D-map refinement like CryoSPARC and Relion. The software UCSF Chimera is developed by the UCSF Resource for Biocomputing, Visualization, and Informatics, supported in part by the National Institutes of Health and is licensed for non-commercial use at no cost.
The Phenix (Python-based Hierarchical ENvironment for Integrated Xtallography)- a comprehensive software package for macromolecular structure determination using crystallographic (X-ray, neutron and electron) and cryo-electron microscopy data, graphical interface includes extensions for Coot and PyMOL.
The Phenix can be downloaded free of charge for Non-Profit Institutions.
The Phenix can be downloaded free of charge for Non-Profit Institutions.
Coot is the standard software for model-building into cryo-EM density, written chiefly by Paul Emsley. The extensions included with the PHENIX GUI allow control of Coot from PHENIX, including automatic loading of models and maps.
PyMOL is a popular open-source molecular graphics software, written by the late Warren DeLano and now maintained by Schrodinger Platform.