Software Directory

Utility for the summation of several powder patterns contained in a Bruker .uxd file. The result is also a .uxd file containing one pattern. Fortran source code included together with an example.

Calculates the bond valence given the length of a particular bond, or the bond length given the valence for inorganic materials. Also calculates the bond valence parameter that results in an exact fit to a given coordination sphere.
Source code is available and a Windows interface would be welcome.

Calculates bond valences for each bond listed in the input file.

A program for calculations and visualizations of contour maps of Bond Valence Sum. Version 2.1
Brown, I.D. (1992). Acta Cryst. B48, 553–572. Waltersson, K. (1978). Acta Cryst. A34, 901–905.

vcif is a simple syntax checker for files in CIF format, including data and dictionary files. It may be used to scan any text file and outputs informative messages about apparent errors in CIF syntax.

vcif2 is an extended version of vcif, the syntax checker for files in CIF format. vcif2 will verify compliance with CIF 1.0, CIF 1.1 or mmCIF file formats; and will accept an arbitrary list of layered DDL1 and DDL2 dictionaries against which units, enumerations, parent-child relationships and category integrity will be checked.

Variable count time data collection for Rietveld refinement.

VEC is a DOS program that comes with the book. Makes predictions for the most probable structural features of valence compounds (Zintl phases). For a given chemical formula crystal chemical, parameters are calculated which are used to predict the average number of homonuclear bonds. Assuming that a structure with an anionic or neutral tetrahedron complex exists, these parameters serve also to select the probable base tetrahedra with which the complex can be constructed. On the screen are shown schematic drawings of the selected base tetrahedra.

Package for visual computing in electron crystallography. Includes: Preliminary processing of electron microscope images, Indexing and measurement of electron difffraction patterns, Determination of the defocus value from a single electron microscope image, Direct-method resolution enhancement of electron microscope images, Simulation of dynamical/kinematical electron diffraction patterns and electron microscope images, 2-, 3- and 4-dimensional FFT, 2-dimensional half-tone-graph, display of 2-, 3- and 4-dimensional Fourier maps Contour mapping of 2-dimensional patterns, Automatic determination of atomic modulation curves in an incommensurate modulated structure

viewer which helps applications within WWW

Bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules.

VESTA is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version, VESTA 3, implementing new features including drawing the external morphology of crystals; superimposing multiple structural models, volumetric data and crystal faces; calculation of electron and nuclear densities from structure parameters; calculation of Patterson functions from structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels; determination of the best plane for selected atoms; an extended bond-search algorithm to enable more sophisticated searches in complex molecules and cage-like structures; undo and redo in graphical user interface operations; and significant performance improvements in rendering isosurfaces and calculating slices.

Complete normal-coordinate calculation on any molecule or crystal, using traditional valence force constants and/or Urey-Bradley force constants.

To facilitate and accelerate sequence analysis, we present, for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphical user interface (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence. In addition, Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.

X-ray Diffraction Analysis Software. Visual CRYSTAL unites 6 major functionalities in one practical and easy-to-use software, making qualitative and quantitative phase analysis by both RIR and RIETVELD full pattern methods. The search-match methods identify easily the compound phases of the sample. The interaction between the identification and the quantification facilitates the interpretation of diffraction data thanks to a progressive reconstruction of the diffractogram and a probability of presence characterizing each phase. The graphic rebuild, adding up the phase full patterns (Pseudo-Voigt function), shows the contribution of each phase to each observed peak or individual count. The profile and structural parameters are refined simultaneously using the Rietveld analysis : non linear least squares solved by Levenberg-Marquardt algorithm which brings the best stability to the process.
Others main features : Background fit, preferred orientation, amorphous phase content calculated without adding a supplementary phase, validation through chemical composition (if available), memorization of the analysis data for later use or verification, macro-commands for repetitive analyses and fully automated production follow-up. VC6 runs with MS Windows NT, XP, Vista and Windows 7. Languages : English, French.

To facilitate and accelerate sequence analysis, we present, for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphical user interface (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence. In addition, Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.

Virtual instrumentation tool for neutron scattering at pulsed and continuous sources

High performance molecular visualization program. Uses hardware accelerated 3D rendering for real-time animation of molecular dynamics trajectories as well as static structures. Can be connected with a running MD simulation for interactive simulation work.

Rietveld analysis