Software Updates

Schrodinger

a suite of tools for small molecule drug discovery. The Schrodinger Suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.

BUSTER

a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

autoPROC

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

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.

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.

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+

a graphical front-end to the LIGPLOT (protein-ligand interactions) and DIMPLOT (protein-protein, domain-domain interactions) programs. The plots generated by these programs can be interactively edited on screen, superposed and printed.