Software Updates

restore

restore is a program for denoising cryogenic electron microscopy images with a convolutional neural network.

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.

MotionCor2

a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.

CUDA

redistributable software libraries to support CUDA applications for Linux.

CrystFEL

a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.

Anaconda

a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.

CCP4

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

SIDESPLITTER

a tool for mitigating local over-fitting during single particle reconstruction.

CCMPred

software for protein residue-residue Contacts from Correlated Mutations PREDicted quickly and accurately.

ChemEX

an analysis program for chemical exchange detected by NMR.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

LigPlot+

the successor to the original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.