Software


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.

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

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.

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.

DiffPy-CMI

DiffPy-CMI is a library of Python modules for robust modeling of nanostructures in crystals, nanomaterials, and amorphous materials. The software provides functionality for storage and manipulation of structure data and calculation of structure-based quantities, such as PDF, SAS, bond valence sums, atom overlaps, bond lengths, and coordinations. Most importantly the DiffPy-CMI package contains a fitting framework for combining multiple experimental inputs in a single optimization problem.

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.

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.

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. 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

TOPAS

Profile and structure analysis software for powder and single crystal data XRD. Profile and structure analysis by integrating a large wealth of profile fitting techniques as well as related applications. Single Line Fitting Indexing (LSI and LP-Search methods) Whole Powder Pattern Decomposition (Pawley and Le Bail methods) Ab-initio structure determination in direct space from powder and single crystal data Rietveld structure refinement Quantitative Rietveld analysis