Software Directory

Sequence analysis batch software

Graphical interface for DBWS, program for Rietveld
refinements. Handles refinement jobs by compiling Input Control
Files (ICF's) for DBWS, importing the CIF files from ICSD, running
the program and showing the graphical results using the shareware
program DMPlot, which plots diffraction patterns.

For original programs see: http://www.ccp14.ac.uk/ccp/web-mirrors/dbws/downloads/young/download_dbws.html

Difference distance matrix plot.

DebUsSy stands for Debye User System and consists of a suite of programs implementing a fast approach to the Debye Scattering Equation (DSE) Analysis for powder diffraction data from nanocrystalline and/or non-ordered materials.
Debussy uses the previously created database(s) and carries out a fast calculation of the diffraction profile of each cluster that contributes to the total pattern, according to a suitable and adjustable size-distribution function. The analysis can be performed on single- or multiple-phase specimens, trying to fit one or more experimental data sets collected with Synchrotron or laboratory X-ray, neutron and electron beams. For all radiation types, the scattering amplitudes/factors of atomic species are encoded into the program. Different options are also available to deal with lattice expansions or contractions variable with the crystal size. Both Chebyshev polynomials and experimentally collected data can be used to manage the background component.

Rietveld refinment with generalized coordinates subjected to geometrical constraints.

DebyeFit is a tool to calculate the Debye or Einstein characteristic temperature of thermal vibrations in crystals from the equivalent atomic displacement parameters (ADPs) of any atom at user’s option that have been obtained at several temperatures. The ADP values are separated into static and dynamic components to get a best fit to the model Debye / Einstein curve. Calculations are based on the Debye, Einstein or mixed model at user’s option. An additional term is first added to the equations to account a possible static disorder. Nonlinear least-square technique is used to refine parameters of the model curve for the set of ADPs observed in the various-temperature structural study. The program provides a good fit up to 0.5 – 2% between the theoretical and observed ADP values. It is quite possible that the best dependence is first achieved within the framework of the Debye or Einstein models between ADPs obtained at different temperatures owing to a simple modification of the formalism

Simulation of plane wave topographs for dislocations

Simulation of section topographs for dislocations

To recognize arrangements of secondary structure elements.

Protein program suite. Name short for density modification.

An algorithm for improvement of the ab initio restoration of biomacromolecular structure from small-angle X-ray scattering data, by consideration of an additional type of `dummy atom', representing the hydration layer is implemented in the program DENFERT.

DENSS is an algorithm that reconstructs the 3D density of a molecule from the 1D solution scattering (SAXS) profile using a novel iterative phase retrieval procedure. DENSS takes as input the 1D scattering data and outputs a standard MRC formatted density map. Several tools and scripts are included for performing data analysis, calculation of the pair distribution function and particle size estimates, averaging of multiple MRC maps, and alignment of PDB atomic models to density maps. An online web server called DENSSWeb is also available at denss.ccr.buffalo.edu.

DENZO is the integration component of a set of programs, HKL, authored by Wladek Minor and Zbyszek Otwinowski.

A program for determining anomalous scattering factors of mixed-oxidation-state species

Differential EXAFS is a new XAS technique dedicated to directly measuring the tiny atomic displacements that arise from such strain-inducing phenomena as magnetostriction, piezoelectricity and thermal expansion. These new experiments have presented the need for new analysis tools to extract and quantify the measured atomic strains, a need that has been addressed by the development of the DEXA code.

For Diamond structures program to refine parameters in the harmonic approximation. refines individual thermal, scale, extinction parameters in diamond type structures.

Visual crystal structure information system for molecular and solid state chemists as well as for surface and material scientists.

Class library providing an object view of mmCIF dictionaries via dictionary object files, with example applications for validation, persistence and attribute access.

part of the CCP14 suite. Indexing program