Software Directory

prototype Perl applications for producing TeX and HTML formatted versions of CIF dictionaries

A program for the analysis of X-ray spectromicroscopy data (Multivariate ANalysis Tool for Spectromicroscopy)

a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals

Mapping of quantitative trait loci (QTLs).

Multiple Alignment of Protein Structures for comparisons of multiple protein structures. Can automatically superimpose the 3d models, detect which residues are structural equivalent and provide the residue-to-residue alignment, calculates a score of structure diversity, which can be used to build a phylogenetic tree.

3D and 2D electron density map visualization. Mainly focused on visualization of ELD calculated from X-ray diffraction data of small molecules, but it will work for small proteins as well.

Generation of "3D" like Fourier electron density contour maps, for small molecule crystallography and powder diffraction

Modelling of powder diffraction data. Full documentation in line. Please note download to [email protected]

The MassEL program allows to calculate masses of individual elements for synthesis of alloys, compounds or mixtures of specific compositions. For instance, in order to get 1 g of the FeSe compound you will have to mix 0.414 g of Fe and 0.586 g of Se. Mass of a specific element (e.g. you have 0.5 g of Fe for your synthesis) can be used as a reference as well.

3D graphic system to display and manipulate atomic structures and low resolution models.

Phase identification from X-ray powder diffraction data. Compares the user's diffraction pattern to the patterns stored in the ICDD PDF database.

supports CIF import

Detection of consensus matches in DNA sequences

MAUD stands for Material Analysis Using Diffraction. It is a general diffraction/reflectivity/fluorescence analysis program mainly based on the Rietveld method, but not limited to.
The main features are:
Written in Java can run on Windows, MacOSX, Linux, Unix (need Java VM 1.6 or later)
Easy to use, every action is controlled by a GUI
Works with X-ray, synchrotron, Neutron, TOF, electrons
Developed for Rietveld analysis, simultaneous multi spectra and different instruments/techniques supported
Ab-initio structure solution integration, from peak finding, indexing to solving
Different optimization algorithms available (LS, Evolutionary, Simulated Annealing, Metadynamics)
Le Bail fitting
Quantitative phase analysis
Microstructure analysis (size-strain, anisotropy and distributions included)
Texture and residual stress analysis using part or full spectra
MEEM and superflip algorithm for Electron Density Maps and fitting
Thin film and multilayer aware; film thickness and absorption models
Reflectivity fitting by different models, from Parratt (Matrix) to Discrete Born Approximation
Works with TEM diffraction images and electron scattering
Several data files input formats
Works and input images from 2D detectors (image plates, CCD)
CIF compliance for input/output; import structures from databases

application for processing and annotating of macromolecular structure data (from the Protein Data Bank)

group of experimental program for 3D and 2D electron density map visualization. The software is mainly focused on visualization of ELD calculated from X-ray diffraction data of small molecules, but it will work for small proteins as well.

Indexing powder patterns by Monte Carlo and grid search.. The 2-theta peak positions extracted from a peak hunting program are used together with the intensities in order to build a pseudo powder pattern to which are compared patterns calculated from the cell parameters proposed by a Monte Carlo or by a grid systematic search process.

Allows the automatic conversion of a section from an electron density map (in CCP4 format) to a ready-to-print postscript file containing a (dithered monochrome) grayscale representation of the electron density with a superimposed contour-line plot.

Ongoing project to create a general tool for simulating neutron scattering instruments. The project is conducted at Ris 006e00610074ional laboratory as part of the RTD project.