Software Directory

Molecular modelling program to visualize and manipulate interactively protein structure files from the Brookhaven Protein Data Bank (PDB) including their hetero-atoms and water molecules. Integrated environment in which statistical analysis as well as 3D observations can be realized.

Extract/convert the information held in GSAS Fourier Map files. Can currently convert GSAS Fourier map files into ASCII, WinGX, Marching Cubes and Project XD Fourier map formats.

FOURDEM is a demonstration program for Fourier synthesis techniques.

Ab initi structure determination from powder diffraction. The crystal structure can be described as any combination of atoms, molecules or polyhedras, without a priori information about the connectivity of these 'building block'.

The FraGen (framework generator) program has been developed for real-space structure solution and designed especially for the generation of extended inorganic frameworks in a given unit cell. It is available from Jihong Yu (jihong@jlu.edu.cn) on request.

A web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets.

Quantitative X-ray diffraction methodology that merges the advantages of existing full-pattern fitting methods with the traditional reference intensity ratio (RIR) method. Like the Rietveld quantitative analysis method, it uses complete diffraction patterns, including the background.

Peak fitting, see CCP14

Visualization of biomolecular structures.

integrated system of programs used in computational chemistry to carry out ab initio, Density Functional Theory and semi-empirical calculations.

A computer graphics program developed for unraveling the relations between different texture parameters and for simulating the basic unrelaxed atomic structures at grain boundary planes in body- and face-centered cubic crystalline materials. The software has been developed using the Visual C++ language, and OpenGL routines have been used for rendering various outputs and implementing an intuitive user interface.
Available as supplementary material or from authors on request.

Genetic Data Environment. An expandable GUI for multiple sequence analysis from the Gilbert Lab Bioinformatics Group

C++11 library that reads and writes CIF files; with Python bindings.

Full Featured Multiple Sequence Alignment Editor and

Full-profile fitting program for Cu-target X-ray powder patterns. Determines integrated intensities and search for proper fundamental parameters. When some parameters, such as the grain size, have large uncertainties, the genetic algorithm has an advantage over conventional least-squares methods in finding the global extremum.

GENFIT is a new computer code featuring an advanced model-fitting capability to analyse small-angle X-ray and neutron scattering data of macromolecular systems. Batches of experimental curves can be simultaneously best fitted using common parameters issued from combinations of models and, if applicable, constrained by physical and/or phenomenological relations.

Fast large scale correlation analysis of genetic structures

Developed for the solution of molecular crystal structures from powder diffraction data. In this package, a genetic algorithm is used for global optimization to search for the structural model. For more efficient calculation time, a modified Bragg R factor is used as the evaluation function for the genetic algorithm. Applications of this program for structure determination of molecular crystals from powder diffraction data are demonstrated with known and previously unknown structures. A friendly graphical user interface (GUI) is used to generate the control file and run the program.

Quick calculation of solvent accessible surface area or solvation energy

Calculates the symmetry operators and special positions for any setting of any space group based on the Hall space group symbol (S.R.Hall (1981) Acta Cryst, A37, 517-525). The input may also be given as a Hermann-Mauguin symbol in the setting-specific form used by the Inorganic Crystal Structure Database. The output lists the special positions with their multiplicities, site symmetries and all equivalent coordinates. Wyckoff letters are not given as they cannot be assigned algorithmically.