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.
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:
CCP4 is an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. CCP4 aims to support the experimental determination and analysis of protein structures.
The Cambridge Structural Database (CSD) is both a repository and a resource for the three-dimensional structural data of molecules generally containing at least carbon and hydrogen, comprising a wide range of organic, metal-organic and organometallic molecules. The specific entries are complementary to the other crystallographic databases such as the PDB, ICSD and PDF. The data, typically obtained by X-ray crystallography and less frequently by neutron diffraction, and submitted by crystallographers and chemists from around the world, are freely accessible (as deposited by authors) on the Internet via the CSD's parent organization's website (CCDC). ConQuest is the primary program for searching and retrieving information from the CSD.
The DIALS project is a collaborativeproject to develop diffraction integration software. 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.
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 (SORTMTZ, SCALA, TRUNCATE) for further data reduction.
PHENIX is a software suite for automated macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This has been made possible by the development of novel algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a set of crystallographic libraries that have been built and made available to the community.
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
SHARP is a computer program for macromolecular crystallography. It operates on reduced, merged and scaled data from SIR(AS), MIR(AS) and MAD experiments, refines the heavy-atom model, helps detect minor or disordered sites using likelihood-based residual maps, and calculates phase probability distributions for all reflections in the data set. autoSHARP is an automated structure solution system - from merged data to automatic model building (uses SHARP as phasing engine).
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. In the program suite: SHELXT extracts the Laue group, cell dimensions and types of element present , solves the structure using data expanded to space group P1, and then uses the P1 phases to find the space group. SHELXS solves small (up to about 100 unique non-hydrogen atom) structures by direct methods. it is based on the classical tangent formula of Karle and Hauptman, but uses phase annealing and includes information from the weak reflections via the negative quartets. etc. etc,-> refer to the SHELX home page
X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. It processes a sequence of adjacent, nonoverlapping rotation images collected from a single-crystal at a fixed X-ray wavelength and recorded by a variety of imaging plate, CCD, pixel and multiwire area detectors; allows arbitrary but fixed orientations of the detector and rotation axis, and only requires that incident beam and rotation axis intercept in one point in the center of the crystal; automatically derives reflecting range, spot width, crystal orientation, symmetry, and cell parameters from the data images. delivers a list of corrected integrated intensities of the reflections occuring in the data images.
XDSAPP is a graphical user interface for the processing of diffraction data sets using XDS. It automates the data hadling 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 data set, 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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