Software Updates

FOCUS

an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.

Xplor-NIH

a package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was derived from XPLOR version 3.851 and contains all of the functionality therein in addition to numerous new features designed to render a highly flexible architecture and foster the rapid and easy development of new functionality.

Xmipp

(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

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.

PHENIX

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

NAMD

a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Molprobity

a protein structure analysis platform offering quality validation for 3D structures of proteins, nucleic acids and complexes.

Geneious

a powerful and comprehensive suite of molecular biology and NGS analysis tools.

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

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.

ARP/wARP

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

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.

CHAP

a tool for the functional annotation of ion channel structures

pdb_extract

a program suite that contains tools and examples for extracting data from many structure determination applications and assembles the data into mmCIF format for wwPDB deposition.

NMRPipe

a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.

CTFFIND 4

a new version of ctffind (a program for finding CTFs of electron micrographs) that should run significantly faster than CTFFIND 3 and may give slightly improved results when processing data from detectors other than scanned photographic film.

pdb_extract

a program suite that contains tools and examples for extracting data from many structure determination applications and assembles the data into mmCIF format for wwPDB deposition.

SBGrid Installer

a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.9 - 10.12. Users can cherrypick a subset of applications for installation on their laptops or desktops. Software updates are highlighted, but users trigger the software update manually at their convenience.