Software Updates

AreTomo3

a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.

DeepFRI

Deep functional residue identification

Starparser

a package implemented in Python to manipulate Relion star files including counting, modifying, plotting, and sifting the data.

cryosparc-tools

a toolkit for interfacing with CryoSPARC.

SHELX-2013

a set of programs for macromolecular phasing. SHELXC provides a simple and fast way to set up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately.

cryosparc-tools

a toolkit for interfacing with CryoSPARC.

MemBrain-Seg

a tool for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).

Rosetta

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

SBGrid Installer

Warp

a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.

ShelXle

a cute graphical user interface for SHELXL.

PHYLIP

a free package of software programs for inferring phylogenies.

autoPROC

a tool that combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data.

XIA2

an expert system for automated reduction of X-Ray diffraction data from macromolecular crystals, making use of existing software (CCP4, XDS, Phenix, CCTBX.) XIA2 is now included with DIALS.

In SBGrid, XIA2 is provided by a few different titles. Run

xia2 --sbapp:l

to see the complete list. The most recent release can usually be found in the latest release of DIALS.

XDS

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.

EMAN2

a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.

ChemEM

a tool that utilizes information from Cryo-EM density and state-of-the-art small molecule force fields to dock small molecules into protein targets.

qFit

a collection of programs for modeling multi-conformer protein structures.

reliontomotools

a set of additional tools for subtomogram analysis in Relion tomo.

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

CryoSieve

an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM).