Software Updates

SBGrid Installer

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

XDSGUI

a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enables XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.

RFdiffusion

an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges.

MicroED tools

for the conversion of microED data collected on TVIPS TemCam-F416, Thermo Fisher CetaD, and Thermo Fisher Falcon III to SMV crystallographic format (*.img)

CryoREAD

CryoREAD is a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.

Napari

is a Python library for n-dimensional image visualisation, annotation, and analysis.

ARP/wARP

an interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.

XDS

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

Topaz

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

Python

a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.

xds_exelixis

XDSGUI

a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enables XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.

Neggia

an HDF5 read plugin for XDS. Neggia presents HDF5 data to XDS in a fully parallelized way, directly and without interconversion and speeds up the processing of HDF5 data.

Durin

XDS plugin for reading HDF5 files following the NeXuS format or those written by Dectris Eiger detectors.

Infernal

(INFERence of RNA ALignment) searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

fpsim2

Simple package for fast molecular similarity searches

TomoTwin-cryoet

a deep metric learning based particle picking procedure for cryo-ET

crYOLO

a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as a standalone program under http://sphire.mpg.de/ and is part of the image processing workflow in SPHIRE.