Created by Frank Schluenzen on Jan 21, 2022 00:21


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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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    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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    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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    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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    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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    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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    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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    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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    pynx — PyNX stands for Python tools for Nano-structures Xtallography.
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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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    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.