Maxwell : Photon Science

Created by Frank Schluenzen, last modified on Jan 03, 2022 17:19


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    adxv — Adxv can be used to display and analyze 2-D area detector data. It is optimized to display X-Ray crystallography diffraction images. The data may be displayed as a 1-D cross section, 2-D image or 3-D surface. Sequential images may be displayed as an animation. The magnification, contrast and color mapping are adjustable. Displayed data may be saved in a variety of formats including ASCII, SMV/IMG, TIFF, JPEG and Postscript.
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    albula — ALBULA is the dedicated software of DECTRIS to display and analyse PILATUS and EIGER data. It consists of the standalone program ALBULA VIEWER and the Python programming interface ALBULA API. 
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    arp_warp — ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination.
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    atsas — The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules.
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    balbes — BALBES is a system for solving protein structures using x-ray crystallographic data. Molecular Replacement (MR) is its core scientific method. BALBES aims to integrate all components, necessary for finding a solution structure by MR, into one system. It consists of a database, scientific programs and a python pipeline. The system is automated so that it needs no user intervention when running a complicated combination of jobs such as model searching, molecular replacement and refinement.
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    BornAgain — BornAgain is a software to simulate and fit neutron and x-ray reflectometry and scattering at grazing incidence (GISANS and GISAXS), using distorted-wave Born approximation (DWBA).
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    ccp4 — ccp4 is actually the Collaborative Computational Project No. 4, synonymous  for the ccp4 software suite for macromolecular crystallography. From the Mission statement: CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.
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    cns — Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.
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    comsyl — COMSYL makes the coherent mode decomposition of synchrotron radiation emitted by electrons passing through an undulator placed in a storage ring. COMSYL permits naturally the statistical analysis and propagation of the cross spectral density along the beamline optics. The coherence properties of the X-ray beam at any point of the beamline are completely given in terms of the eigenvalues and coherent modes of the cross spectral density (copied from https://github.com/mark-glass/comsyl ).
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    condor — Condor, an open-source simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model. The software enables researchers to test whether their envisaged imaging experiment is feasible, and to optimize critical parameters for reaching the best possible result.
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    conuss — A scientific application to calculate nuclear resonant scattering spectra and fit relevant parameters to experimental data obtained using synchrotron Mössbauer spectroscopy, conventional Mössbauer spectroscopy, nuclear forward scattering, nuclear Bragg/Laue scattering, and grazing incidence nuclear resonant scattering.
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    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.
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    dawn — Data Analysis WorkbeNch (DAWN) is an eclipse based workbench for doing scientific data analysis.
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    dials — The DIALS project is a collaborative endeavour to develop new diffraction integration software to meet the data analysis requirements presented by these recent advances. There are three end goals: to develop an extensible framework for the development of algorithms to analyse X-ray diffraction data; the implementation of algorithms within this framework and finally a set of user facing tools using these algorithms to allow integration of data from diffraction experiments on synchrotron and free electron sources.
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    dioptas — Python based GUI-Program for integration and exploration of 2D x-ray diffraction images. 
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    DirAx — DirAx is a program for indexing of single crystal data as explained in Duisenberg, A.J.M.(1992). J. Appl. Cryst. 25, 92-96 (IUCR journal webpage) .
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    dpdak — DPDAK is an open source (GPL) tool developed for (online) analysis of large sequences of small angle scattering data - but can be used for other data as well. It is written in Python and runs on Windows and Linux. The development is a cooperation between DESY and MPIKG.
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    fdmnes — The aim of the FDMNES project is to supply to the community a user friendly code to simulate x-ray spectroscopies, linked to the real absorption (XANES, XMCD) or resonant scattering (RXD) of the synchrotron radiation. This ab initio approach, wants to eliminate all the methodological parameters. First mainly mono-electronic, using the functionnal density theory (DFT), it includes now multi-electronics advances with the use of the time dependant DFT (TD-DFT) for a better taking into account of the excited states linked to the photon-matter interaction. It includes also the Hubbard correction (LDA+U) for a better description of the so called correlated materials.
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    genesis — GENESIS 1.3 is a time-dependent three-dimensional FEL code. It is focused to simulate single-pass free-electron lasers, both FEL amplifier and SASE FEL, although the flexible input can be used to easily extend the capacity of GENESIS 1.3 to cover FEL oscillators or multistage setups.
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    geopixe — GeoPIXE incorporates the Dynamic Analysis method for real-time PIXE/SXRF spectral deconvolution to project quantitative PIXE/SXRF elemental images from list-mode data, and tools for image exploration, spectra extraction for quality control, and for multi-layered targets, using an efficient Windows/Linux graphical user interface.
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    hexrd — The HEXRD project is developing a cross-platform, open-source library for the general analysis of X-ray diffraction data. This includes powder diffraction, Laue diffraction, and High Energy Diffraction Microscopy (a.k.a. 3DXRD, multi-grain rotation method) modalities.
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    IceNine
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    ImageD11 — ImageD11 is for identifying individual grains in spotty area detector diffraction images. It finds the spots and helps you to try to index them.
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    Impact-Z — Impact-Z is a 3D parallel/serial PIC code based on multi-layer object-oriented design. Impact-Z can treat intense beam propagating through drifts, magnetic quadropols or solenoids, ... using linear map or nonlinear Lorentz integrator.  The installation on Maxwell provides both Impact-Z and Impact-T.
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    Maud
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    mosflm — MOSFLM can process diffraction images from a wide range of detectors and produces, as output, an MTZ file of reflection indices with their intensities and standard deviations (and other parameters). This MTZ file is passed onto other programs of the CCP4 program suite (POINTLESS, SORTMTZ, AIMLESS, CTRUNCATE) for further data reduction.
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    oasys — OASYS (OrAnge SYnchrotron Suite) is a graphical environment for optic simulation software used in synchrotron facilities, based on Orange 3.
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    olex2 — Olex² is an immensely powerful Crystallography program, which handles very complex crystallographic tasks through an intuitive GUI. The graphical user interface is the result of 10 years of striving to provide the best possible experience tomodellingeven the most challenging structures with ease. 
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    PanDDA — Pan-Dataset Density Analysis. Multi-dataset crystallographic analysis for the identification of ligand binding and structural events
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    phenix —  PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
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    platon —  PLATON is a versatile SHELX97 compatible multipurpose crystallographic tool. Most PLATON features complement those available in the excellent and widely distributed SHELX97 package for crystal structure determination and refinement.
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    pyfabio
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    pyFAI — pyFAI is an azimuthal integration library that tries to be fast (as fast as C and even more using OpenCL and GPU). It is based on histogramming of the 2theta/Q positions of each (center of) pixel weighted by the intensity of each pixel, but parallel version uses a SparseMatrix-DenseVector multiplication. Neighboring output bins get also a contribution of pixels next to the border thanks to pixel splitting.
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    pyMca — X-Ray Fluorescence Analysis Toolkit and Application. Stand-alone application and Python tools for interactive and/or batch processing analysis of X-Ray Fluorescence Spectra. Graphical user interface (GUI) and batch processing capabilities provided.
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    pynx — PyNX stands for Python tools for Nano-structures Xtallography.
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    sasfit — SASfit has been written for analyzing and plotting small angle scattering data. It can calculate integral structural parameters like radius of gyration, scattering invariant, Porod constant. Furthermore it can fit size distributions together with several form factors including different structure factors. Additionally an algorithm has been implemented, which allows to simultaneously fit several scattering curves with a common set of (global) parameters. This last option is especially important in contrast variation experiments or measurements with polarised neutrons. The global fit helps to determine fit parameters unambiguously which by analysing a single curve would be otherwise strongly correlated.
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    shelx — SHELX is a set of programs for the determination of small (SM) and macromolecular (MM) crystal structures by single crystal X-ray and neutron diffraction.
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    srw — SRW (Synchrotron Radiation Workshop") is a physical optics computer code for calculation of detailed characteristics of Synchrotron Radiation (SR) generated by relativistic electrons in magnetic fields of arbitrary configuration and for simulation of the radiation wavefront propagation through optical systems of beamlines.
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    tomopy — Tomographic reconstruction creates three-dimensional views of an object by combining two-dimensional images taken from multiple directions, for example in how a CAT (computer-aided tomography) scanner allows 3D views of the heart or brain.
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    XChemExplorer — XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery.
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    xds — XDS is a program package written for the "reduction" of 2-dimensional data images ("frames") obtained from crystals irradiated with monochromatic X-rays.
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    xdsapp — XDSAPP (Sparta et al., 2016) is a graphical user interface for the easy and convenient processing of diffraction data sets using XDS. It automates the data processing and generates graphical plots of various data set statistics provided by XDS and other programs. By incorporating additional software, further information on certain features of the dataset, such as radiation decay or the presence of pseudo-translational symmetry and/or twinning is provided. Intensity files suitable for CCP4, SHELX and CNS are automatically generated.
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    xdsgui — XDSGUI is a GUI (graphical user interface) for XDS that is supposed to help both novice and experienced users. It graphically displays the ASCII and cbf files that XDS writes, and can run useful shell commands with a simple mouse click. The design goal of the program is to enable XDS data processing without the commandline, and to supply additional graphical information, in a simple, user-modifiable and user-extensible way.
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    xia2 — xia2 is an expert system to perform X-ray diffraction data processing on your behalf, using your software with little or no input from you. It will correctly handle multi-pass, multi-wavelength data sets as described later but it is not a data processing package. Specifically, if you use xia2 in published work please include the references for the programs it has used, which are printed at the end of the output. The system was initially written to support remote access to synchrotron facilities, however it may prove useful to anyone using MX.
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    xmimsim — XMI-MSIM is an open source tool designed for predicting the spectral response of energy-dispersive X-ray fluorescence spectrometers using Monte Carlo simulations. It comes with a fully functional graphical user interface in order to make it as user friendly as possible. Considerable effort has been taken to ensure easy installation on all major platforms.
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    xop — XOP (X-ray Oriented Programs) is a widget-based driver program that is used as a common front-end interface for computer codes of interest to the synchrotron radiation community.
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    xrt — Package xrt (XRayTracer) is a python software library for ray tracing and wave propagation in x-ray regime. It is primarily meant for modeling synchrotron sources, beamlines and beamline elements. Includes a GUI for creating a beamline and interactively viewing it in 3D.