Software Updates

CARA

(Computer Aided Resonance Assignment) an application for the analysis of NMR spectra and computer-aided resonance assignment.

SPIDER

(System for Processing Image Data from Electron microscopy and Related fields) a large image processing suite for electron microscopy.

Geneious

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

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.

DUI

(Dials User Interface) a GUI to allow the general user to run DIALS tools and inspect the output without resorting to detailed command-line usage.

ATSAS

a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.

PEET

(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

Schrodinger

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

ProDy

a protein structural dynamics analysis software package.

ProDy is installed as a module within python.

Rasmol

a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

AutoDock Vina

a program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

py4xs

a python package for processing x-ray scattering data, first developed at the X9 beamline at NSLS, but revised multiple times and now in use at the LiX beamline at NSLS-II.

O

a model building application for X-ray crystallography.

iMosflm

a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.

NMRFAM-Sparky

a new version of Sparky renamed because NMRFAM, through the generous allowance of Tom Ferrin and Tom Goddard of UCSF, has taken over the original Sparky for continuous development to support advances in the biomolecular NMR field.

AutoDock Vina

a program for drug discovery, molecular docking, and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

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.

Foldseek

a program that enables fast and sensitive comparisons of large structure sets.

adxv

a tool that displays protein crystallography X-ray diffraction data. The data may be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data files may be saved in tiff or postscript format.