Crystallographic software list
ABSCYL Absorption correction for cylinders (very handy for needle shaped crystals). Program by JH Reibenspies at Texas A&M.
ABSEN 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.
ABSORB 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-7 and ABSORB-GUI 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.
ACNUC ACNUC is a retrieval system for the nucleotide sequence databases.
AC_prediction 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
Acquisition of Images Digitization software.
ADM 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.
ALIGN Superimposition of protein coordinates accounting for insertions and deletions.
Alscript 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 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
Amas Automatic analysis of multiple protein sequence.
AMBER Assisted Model Building with Energy Refinement.
Amps Multiple protein sequence alignment and flexible pattern.
ANAELU Software package ANAELU (analytical emulator Laue utility) has been created for aiding the interpretation of two-dimensional X-ray diffraction patterns produced by textured (bulk and nanostructured) samples. ANAELU is composed of three interconnected applications, corresponding to three crystallographic tasks: structure representation, two-dimensional pattern analysis and diffraction simulation.
ANODE The program determines anomalous (or heavy-atom) densities by reversing the usual procedure for experimental phase determination. Instead of adding a phase shift to the heavy-atom phases to obtain a starting value for the native protein phase, this phase shift is subtracted from the native phase to obtain the heavy-atom substructure phase.
ANSIG Analysis of NMR spectra. Tool for analysis and assignment of multidimensional spectra.
ANTHEPROT Protein analysis. Web on-line tool.
ARITVE Modelling amorphous structures by a Rietveld-type refinement of the atomic coordinates.
ARP/wARP ARP/wARP is used for automated building and refinement of protein structures. Real space pattern recognition, refinement and model update are combined with reciprocal space refinement to construct and improve protein models. ARP/wARP can also be used for ab initio structure solution of metalloproteins at high resolution.
ASCALAPH Ascalaph is a general purpose molecular modeling suite that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. It can interact with external molecular modeling packages (MDynaMix, NWChem, CP2K and PC GAMESS/Firefly).
ASF88 For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system.
Asf88win For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system.
Assp The program takes a multiple protein sequence alignment and estimates the range in accuracy that one can expect for a "perfect" secondary structure prediction made using the alignment.
ATHENA, ARTEMIS, HEPHAESTUS This software package is based on the IFEFFIT library of numerical and XAS algorithms. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner.
ATOMS Display of atomic structures.
ATSAS New developments in version 2.4 of the ATSAS package for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described.
AutoDep Autodep is a tool designed for the deposition into the Protein Data Bank of molecular coordinates data generated by the experimental procedures, viz. protein crystallography, NMR, EM.
AutoDock Suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Of use for X-ray crystallography, structure-based drug design, lead optimization, virtual screening (HTS), combinatorial library design, protein-protein docking, chemical mechanism studies.
AUTO_XPL Automates many of the computational steps involved in using X-PLOR.
AXES Program for X-ray powder diffraction data evaluation that is specially designed for peak-shape analysis and data preparation for Rietveld refinement in connection with the FULLPROF program.
AZARA Analysis of NMR spectra. Suite of programs for the processing of multidimensional spectra