CryoEM

The majority of CryoEM packages listed below and available in PReSTO is mentioned in the recent publication Using RELION software within the Scipion framework by Dustin Morado, Marta Carroni and José Maria de la Rosa-Trevin from CryoEM SciLifeLab Stockholm and Grigory Sharow from MRC Laboratory of Molecular Biology in Cambridge.

Please see the page cryoSPARC on Berzelius for instructions on how to start cryoSPARC on the Berzelius system.

To improve this documenation on Cryo-EM softwares in PReSTO we want support from the Swedish Cryo-EM community! Please and suggest improvements perhaps sharing an example script, links to recent tutorials, or other information that may help Cryo-EM newcomers. For instance here is a script to lftp to transfer data from Umeå ftp server ucem.kbc.umu.se to NSC Berzelius. Exchange USER and PASSWORD, and update REMOTE_DIR and LOCAL_DIR, change permissions by chmod 755 mirror_lftp_share.sh and run in the background by ./mirror_lftp_share.sh &.

CryoSPARC

CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy used in research and drug discovery pipelines. Use module avail CryoSPARC to find latest version at NSC Berzelius or Tetralith.

Scipion

Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM) published by José Maria de la Rosa-Trevin and colleagues in 2016 and 2021. It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Scipion is available from the PReSTO menu.

cisTEM

cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. It 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.

Relion

Relion for REgularised LIkelihood OptimisatioN is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology and published in 2012. Online documentation and gihub repository. Relion-CPU and Relion-GPU is available from the PReSTO menu.

Gctf

Gctf is a GPU accelerated program for accurate estimation of the contrast transfer function (CTF) written by Kai Zhang

Gautomatch

Gautomatch is a GPU accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates written by Kai Zhang.

MotionCor2

MotionCor2 is multi-GPU accelerated software that corrects for electron beam-induced sample motion presented here and published in 2013

Ctffind

Ctffind finds CTFs of electron micrographs written by Niko Grigorieff and colleagues presented in detail online. Ctffind is available from the PReSTO menu.

EMAN2

EMAN a scientific image processing suite intended for data from transmission electron microscopes. EMAN2 is available from the PReSTO menu.

crYOLO

crYOLO is an application for fast and accurate cryo-EM particle picking. It’s based on convolutional neural networks and utilizes the popular You Only Look Once (YOLO) object detection system.

Xmipp

Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.