Software Updates

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

a tool 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

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

Napari

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

ARP/wARP

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

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.

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

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

Infernal

(INFERence of RNA ALignment) a program that 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

a 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.