Software Directory

Review on suites of programs for small molecules

Solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data.

Generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file.

Macintosh application that provides a user friendly interface allowing analysis of several proteins at the same time.

For the routine analysis of crystallographic texture by neutron diffraction at Chalk River Laboratories.

Symmetrizes a group of atoms whose coordinates, either orthogonal or oblique, are given in input. It prints out information about the given set of atoms and information concerning its symmetry: the symmetrized orthogonal coordinates together the point group (PG), the labels and the equivalent positions. Some quantities showing the goodness-of-fit are also printed: the rms on the coordinates, the molecular rms, the maximum deviation of the coordinates of the atom from the symmetrized ones and the continuous symmetry measure (CSM) for the whole PG and for the single elements of the PG.

an iOS app for th front end to ISPyB, a laboratory information system for macromolecular crystallography synchrotron beamlines.

Small suite of test files conforming (or not) to STAR/CIF syntax rules and designed as an aid to parser development

Tool for digitizing data from an image of graph or plot from Ron Jones.

A package for analysis of convergent beam electron diffraction (CBED) patterns;
in particular, for refinement of lattice parameters based on multiple CBED patterns.

Calculates x-ray specular reflection from multilayers at grazing incidence. It can account for small interface roughness using Nevot and Croce's method, and the high rms roughness can be simulated with transition layers.

Tessel2 is a 3D "compiler" to produce crystal and molecular models, parametric surfaces and several forms of sphere tesselations.

cell symetry checking, see CCP14.

From data processing to structure solution, modeling, refinement

Software and databases for thermodynamic calculations

Protein TOPological comparison program which detects whether there are structural similarities between two proteins.

General non-linear least squares system driven by a scripting language. Applied to solid state chemistry and optimization. Contains minimization routines wrapped by a computer algebra system; it is this foundation that makes subject dependent modules such as Rietveld refinement shine. Academic version of BRUKER-AXS TOPAS.

Package for calculation of geometrical and topological properties of crystal structures.

Topological analysis program for experimental static electron density based on Hansen-Coppens multipole formalism

Phi-psi values from a PDB file. Author: Andrew CR Martin at UCL.