Software


ARCIMBOLDO

Ab Initio macromolecular phasing has been traditionally limited to small proteins at atomic resolution (1.2Å or better unless heavy atoms are present). ARCIMBOLDO constitutes a general method for 2Å data, based on combination of location of model fragments like small ?-helices with PHASER and density modification with SHELXE, distributed over a grid of computers.

Atomic Simulation Environment (ASE)

The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.

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.

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.

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:

CCP4

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.

COD (Crystallographic Open Database)

Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers. As of 2016/12/13, there are 369600 entries in the COD

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]

CSD (CCDC)

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.

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.

DIALS

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.

Fox/ObjCryst++

The FOX program was made for ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Its most interesting features for ab initio structure determination are: * a versatile description of the crystal contents: either isolated atoms , molecules described using a bond length, bond angles and dihedral angles, and polyhedra for inorganic compounds. You can describe your structure by using any combination of groups of atoms, using a chemist's or crystallographer knowledge about the connectivity in your sample to constrain possible solutions.. * an automatic correction for special positions and shared atoms between polyhedra, suitable for global optimization algorithms. * the ability to use simultaneously multiple powder patterns (X-rays, neutrons), as well as single crystal data (e.g. extracted from a powder pattern) * smart global optimization algorithms which can get out of false minima. * a graphical interface (see the screenshots) with a 3D crystal structure view, with live updates during the optimization process.

ICSD

Inorganic Crystal Structure Database, containing about 185,000 peer-reviewed data entries of inorganic and related structures, including their atomic coordinates dating back to 1913. It is produced cooperatively by FIZ Karlsruhe and the National Institute of Standards and Technology (NIST).

Materials Studio

Materials Studio is a modeling and simulation environment designed to allow to predict and understand the relationships of a material’s atomic and molecular structure with its properties and behavior. With it one can construct, manipulate and view models of molecules, crystalline materials, surfaces, polymers, and mesoscale structures. Materials Studio includes quantum, atomistic (or “classical”), mesoscale, and statistical methods that enable one to evaluate materials at various particle sizes and time scales. It also includes tools for evaluating crystal structure and crystal growth.

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 (SORTMTZ, SCALA, TRUNCATE) for further data reduction.