Crystallographic software list
BABEL Program designed to interconvert a number of file formats currently used in molecular moldeling. rpm for Linux available at ftp site.
Balls & Sticks Balls & Sticks is a program to create 3D image and animation of crystal structures. It was designed with the emphasis on ease of use. It imports CIF files, then polyhedra and bonds can be defined by mouse-cliking on end-member atoms. All the other operations are also implemented via the graphical user interface.
BALSAC Build and Analyze Lattices, Surfaces, And Clusters,
Baxmap Visualisation , transformation and analysis of crystallographic coordinates. Allows for both crystallographic and non-crystallographic transformations, with such modifications as bond lengths, angles and torsions, as well as reorientations of molecules within the unit cell. Written by Ian Baxter at Imperial College.
BayesApp A web site for indirect transformation of small-angle scattering data. No user input is necessary beyond the experimental data. Results of the analysis can be downloaded from the web site in the form of ASCII files.
BayesApp: update An update for BayesApp, a web site for analysis of small-angle scattering data, is presented. Most importantly the indirect transformation of data now includes an option for a maximum-entropy constraint in addition to the conventional smoothness constraint. A correction for slit smearing is possible, and options for calculation of the scattering intensity from simple models as well as estimation of structure factors for nonspherical objects have also been added.
BCA spreadsheets Series of Crystallographic Spreadsheets in EXCEL format collated by David Taylor and the Industrial group of the BCA (British Crystallographic Association). Includes calculations relating to thin films, pattern and peak position correction, manual search match sheet, X-ray penetration, size/strain calculation.
BCC For BCC structures program to refine parameters in the harmonic approximation. refines individual thermal, scale, extinction parameters in BCC type structures.
BEAM-ish Graphical user interface for processing of multiple superfine φ-sliced diffraction images for mosaicity calculation.
Beamline Scheduling Software (BSS) Beamline Scheduling Software (BSS) has been developed for the schedule management and equipment control of the RIKEN Structural Genomics Beamlines I and II (BL26B1 and BL26B2 at SPring-8).
BenchFFT Benchmark of a large number of publicly-available FFT implementations, both in C and in Fortran, and measures their performance and accuracy over a wide range of transform sizes.
Better User Group Software The main activity of the NOBUGS group has so far been the organization of a series of conferences. The aim of these conferences is to foster collaboration between IT professionals working at X-ray and neutron sources around the world. This collaboration should yield better data acquisition and data analysis software for the users of such facilities. This in turn will increase user productivity and thus maximize the scientific result to be obtained from the large investment required to build and maintain X-ray or Neutron facilities.
BGMN Rietveld refinement program. Fully automatic calculation which requires no user interaction. Automatic correction of strong and multiple preferred orientation with spherical harmonics. Common model for anisotropic peak broadening. Phase analysis of disordered layer silicates by implementation of advanced real structure models. Correction of microabsorption with the Brindley model. Easy-to-use model for refinement of site occupancy. Refinement of amorphous content with an internal standard. Special features for structure investigation and refinement. Related programs EFLECH/INDEX. Full demo available on site.
Biological software EBI Archive for biological software at EBI.
BIOMOL In the Crystallography group at the University of Groningen, Netherlands a number of programs have been developed for the manipulation of Crystallographic data. These programs have been bundled in a package, known as the BIOMOL package.
Bioperl Bioperl is an association of developers of public domain Perl tools for computational molecular biology
BLANC Collection of programs for macromolecular structure determination. Among others the suite contains the programs SFCHECK, MOLREP, CONTACT, LIBCHECK, MAKECIF, EMIN, MIR, SIR,TRAHALO.
BLAST Sequence similarity measurement.
Blueprint XAS Blueprint XAS is a new Matlab-based program developed to fit and analyse X-ray absorption spectroscopy (XAS) data, most specifically in the near-edge region of the spectrum.
Blu-Ice and Distributed Control System (DCS) The Blu-Ice and Distributed Control System (DCS) software packages were developed to provide unified control over the disparate hardware resources available at a macromolecular crystallography beamline. Blu-Ice is a user interface that provides scientific experimenters and beamline support staff with intuitive graphical tools for collecting diffraction data and configuring beamlines for experiments.
BOB Blast output Browser.
Bond Valence Wizard Stand-alone program which predicts bond lengths by the Bond Valence Method. Complex structures up to 6480 different atomic positions are acceptable. Uses GUI and user-extendible database for unit length parameters which bases on I.D.Brown's tables
Bonsu Versatile tool for phase retrieval and data visualization in both two and three dimensions. The software should be of use to the coherent diffraction imaging community. The developers aim to provide further enhancements in future releases with additional algorithms being incorporated.
BornAgain Open-source research software to simulate and fit neutron and x-ray reflectometry, off-specular scattering, and grazing-incidence small-angle scattering.
BRAGI Interactive protein modelling and display program.
BRASS Bremen Rietveld Analysis and Structure Suite. Quantitative, qualitative and structural analyses based on powder diffraction data and crystallographic structure models. Structure model plots and crystal chemical calculations. Crystallite size and microstrain determination. Provide a common platform for tasks which are often designated stand-alone programs.
BREADTH A simple integral-breadth-type program for analyzing diffraction line broadening. The program calculates domain size and strain from input integral breadths of at least two physically broadened diffraction-line profiles according to the Warren-Averbach approach.
BRL Calculates multiple Bragg diffraction of x-rays by perfect crystals. Simulates up to 12-wave dynamical Bragg diffraction of x-rays from plate shaped crystals including the cases of x-ray waves grazing along the plate surface and the Bragg angles being close to 90 degrees.
BSSB: BLAST Server Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs, but none of the existing tools for processing BLAST output provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed tool BLAST Server for Structural Biologists (BSSB), which maps a BLAST output onto the three-dimensional structure of the subject protein.
BUNYIP Program for detecting missing symmetry elements in crystal structures.