Software Directory

2D and 3D image processing

3D reconstruction home page. 3D visualization software

New web based browser, 3DBbrowse, makes it even simpler to search and retrieve data from the
Protein Data Bank (PDB).

3DBVSMAPPER is a program that calculates bond-valence sums and bond-valence energies for crystal structures. It calculates both bond valence/energy at atomic positions and also at a 3-D grid of points to map ion conduction pathways and likely atomic positions. The program also calculates total energies and the global instability index.

Absorption correction for cylinders (very handy for needle shaped crystals). Program by JH Reibenspies at Texas A&M.

Study and display of crystal structures, thermal ellipsoid plots, mouse based interactive editing of Shelx files with auto atom sort. RASTEP and RENDER have been added to the system giving realistic rendered 3D pictures from the same view as ORTEX direct from Shelx.INS files.

Brennan-Cowan X-ray absorption, reflection and dispersion calculation. Calculates f' and f'' based on theoretical work of Cromer and Liberman calculates Rayleigh and Compton cross-section based on McMaster.

ABSORB is a program to calculate and apply absorption corrections to single-crystal X-ray intensity data, has been reconfigured to allow it to be called directly from external data processing programs. ABSORB-GUI has been developed to allow much easier specification of standard experiments.

Program for the analysis of atomic mobility. AC_prediction implements automatic decision-making procedures based on atomic shift magnitudes in unrestrained refinement to highlight the specific residues that are likely to harbour alternative conformations and that hence require checking via electron density maps

ACNUC is a retrieval system for the nucleotide sequence databases.

Digitization software.

deposition tool for depositing macromolecular structures in the Protein Data Bank

for checking the format consistency of coordinates and creating validation reports about a structure before deposition in the Protein Data Bank

Solution including device control, the diffractogram evaluation, qualitative and quantitative phase analysis, indexing, lattice parameter refinement, crystal size evaluation, micro-stress analysis, profile analysis and pattern simulation.

Superimposition of protein coordinates accounting for insertions and deletions.

Alscript is a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. Alscript does not support point-and-click, but has a scripting language to allow complex effects.

Altwyk is a stand-alone program which produces the general position and Wyckoff positions for any space group symbol listed in International Tables for Crystallography, Vol. A (1983). Altwyk can currently process over 1,000 of them, probably covering all actual literature cases, but we are still implementing new odd symbols. Written by Y. Le Page and S. Raymond

Automatic analysis of multiple protein sequence.

Assisted Model Building with Energy Refinement.

Multiple protein sequence alignment and flexible pattern.