Software


ATSAS

ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules. It includes multiplatform data manipulation and displays tools, programs for automated data processing and calculation of overall parameters, usage of high- and low-resolution models from other structural methods, algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and enhanced tools to analyse data from mixtures and flexible systems.

AUTOPROC

autoPROC is a set of tools and programs to automate the whole range of steps involved in data processing: analysis of collections of images and image headers, indexing of diffraction images, determination of accurate cell parameters, integration of a series of images, processing of multi-sweep datasets, production of files of intensities and amplitudes in various formats (MTZ, Scalepack), analysis of anomalous signal, automatic determination of most likely space group symmetry.

Avizo

3D analysis software for scientific and industrial data. Different application areas: Materials Science, Quality Assurance in Industrial Environments, Electronics, Digital Rock Analysis etc. It enables users to perform interactive visualization and computation on 3D data sets. The Avizo interface is modelled on the visual programming. Users manipulate data and module components, organized in an interactive graph representation (called Pool), or in a Tree view. Data and modules can be interactively connected together, and controlled with several parameters, creating a visual processing network whose output is displayed in a 3D viewer. With this interface, complex data can be interactively explored and analyzed by applying a controlled sequence of computation and display processes resulting in a meaningful visual representation and associated derived data.

BINoculars

BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a 2D X-ray detector. The intensity of each pixel of a 2D-detector is projected onto a 3-dimensional grid in reciprocal lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution datasets and results in a significant reduction of the size of the dataset. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques.

BornAgain

BornAgain is a software package to simulate and fit small-angle scattering at grazing incidence. It supports analysis of both X-ray (GISAXS) and neutron (GISANS) data. Its name, BornAgain, indicates the central role of the distorted wave Born approximation in the physical description of the scattering process. The software provides a generic framework for modeling multilayer samples with smooth or rough interfaces and with various types of embedded nanoparticles.

BUSTER

BUSTER is a framework for automatic refinement of macromolecules. It uses maximum-likelihood (ML) and maximum-entropy (ME) techniques to overcome two major shortcomings encountered by classical methods (least-squares (LS) + difference maps) when dealing with the refinement and completion of partial structures:

CONUSS

The CONUSS software package provides evaluation methods for data obtained by nuclear resonant scattering techniques. It is used for the interpretation of time or energy spectra from coherent elastic nuclear resonant scattering, i.e., forward scattering and Bragg/Laue scattering,

CrysAlis Pro

Data collection and data processing software for small molecule and protein crystallography. Main features: automatic crystal screening, data collection and strategy modules. It provides the user with information regarding the unit cell, intensity estimation by resolution range and suggested frame exposure times for the full data collection.

CRYSTAL

Computational tool for solid state physics and chemistry. The CRYSTAL package performs ab initio calculations of the ground state energy, energy gradient, electronic wave function and properties of periodic systems. Hartree-Fock or Kohn- Sham Hamiltonians (adopting an Exchange-Correlation potential following the DFT postulates of ) can be used. Systems periodic in 0 (molecules, 0D), 1 (polymers, 1D), 2 (slabs, 2D), and 3 dimensions (crystals, 3D) are treated on an equal footing. In each case the fundamental approximation made is the expansion of the single particle wave functions ('Crystalline Orbital', CO) as a linear combination of Bloch functions (BF) defined in terms of local functions, i.e. Atomic Orbitals.

CrystFEL

CrystFEL is 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. CrystFEL comprises programs for indexing and integrating diffraction patterns, scaling and merging intensities, simulating patterns, calculating figures of merit for the data and visualising the results. Supporting scripts are provided to help at all stages, including importing data into CCP4 for further processing. [From: the Website]

DAWN

DAWN, the Data Analysis WorkbeNch, is an Eclipse based application for scientific data analysis. It comes with a range of tools for visualization (1D, 2D and 3D), code development environments (for Python, Jython and Eclipse plug-ins) as well as processing workflows with visual algorithms for analyzing scientific datasets. It is primarily developed at Diamond Light Source, but external contributions are most welcome! DAWN is distributed freely and is released under the Eclipse Public License.

Demeter

Demeter is a comprehensive system for processing and analyzing X-ray Absorption Spectroscopy data. It contains several packages such as Athena, Artemis and Hephaestus, which are widely used in the XAFS community.

DL_EXCURV (formerly EXCURVE)

Data analysis of EXAFS spectra using the fast spherical wave method. It provides an integrated environment for the analysis of EXAFS spectra while delivering a platform for the fast spherical wave method. The current version is based on this method for single scattering, but uses the method of Lee and Pendry (1975) for the exact polarisation dependent theory. Multiple scattering has options to use several methods. It allows fitting of both background-subtracted, and normalised total absorbance spectra. In the latter case the program calculates the atomic contribution of the spectrum (whole-spectrum fitting). The purpose of the program is to find a structural model of a material which agrees with the available XAFS spectra. This program (without GUI) was formerly called EXCURVE and is the one installed at the ESRF

FEFF9

Condensed matter code for modelling x-ray and electron spectroscopies and materials properties. FEFF is an automated program for ab initio multiple scattering calculations of X-ray Absorption Fine Structure (XAFS), X-ray Absorption Near-Edge Structure (XANES) and various other spectra for clusters of atoms. The code yields scattering amplitudes and phases used in many modern XAFS analysis codes, as well as various other properties. in FEFF9 there are several new spectroscopies which can be calculated with FEFF 9, including electron energy loss spectra (EELS) and non-resonant inelastic x-ray scattering (NRIXS). In addition, there are a variety of improvements. These include; (1) ab initio Debye-Waller factors; (2) improved treatment of inelastic losses; (3) an improved treatment of the core-hole interaction; and (4) more accurate treatment of crystalline systems with k-space calculation of the Green's function. FEFF9 comes with the JFEFF GUI.

FIT2D

FIT2D is a general purpose 1 and 2 dimensional data analysis program. It is used for both interactive and "batch" data processing, and is used for different purposes. Calibration and correction of detector distortions is one of the main uses of FIT2D. Difficult data analysis problems may be tackled using fitting of user specified models. To enable model fitting to be performed on a wide variety of input data, many other more basic data analysis operations are also available. A wide variety of performant graphical display methods are available.