Software Updates

SPIDER

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

XDrawChem

a two-dimensional molecule drawing program for Unix operating systems that can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.

TimeScapes

a Python-based program package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems.

ScÅtter

a JAVA-based application for basic analysis of SAXS datasets. Scatter is developed by Robert Rambo at the Diamond Light Source (Didcot, UK). The program was previously developed at the SIBYLS beamline (12.3.1) of the Advanced Light Source, Berkeley, CA.

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.

Priism/IVE

a graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism.

NAMD

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

Dynamo

a software environment for subtomogram averaging of cryo-EM data.

DSSR

(Dissecting the Spatial Structure of RNA) a software tool for dissecting the spatial structure of RNA.

OpenJDK

(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).

vtk

(Visualization Tool Kit) a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods, as well as advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

XRayView

a tool that uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.

EPMR

a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc.