Software Directory

Neutron Scattering Software

API which works with the NeXus Data Definition Language. Nexus is a portable data exchange format for neutron and X--ray scattering.

A description of the NeXus data format for X-ray and neutron scattering and muon spectroscopy

A free open-source Igor Pro-based program for reduction of two-dimensional scattering data from area-detector small- and wide-angle scattering instruments to one-dimensional lineouts.

Chemistry Structure

Simulation of short-range Al/Si order in framework

For protein structure model-building, visualization, validation and analysis ... Auto-fit residues' side-chain against density data (experimental function) - Solid surface creating and electrostatic potential, hydrophobic force coloring - Hardware stereo view supported - Side by side stereo view

A program for fast building of distance-constrained starting configuration files for RMCA modelling.

Program for optical-activity calculations.

Interface for refinements in olex2.refine (cctbx) using any type of non-spherical scattering factors. Includes interface for many QM codes to calculate wavefunctions on the fly for tailor-made scattering factors and partitioning. Also provides tools to calculate many properties available from the wavefunctions used and visualize them.

NSXTool is a software for reducing single-crystal data. It implements in a single application all the steps necessary for integrating the intensities of Bragg's peaks prior to structure determination. Some of the key features already implemented are fast data reading, peak search, peak indexing, UB matrix determination, instrumental offsets refining, space group determination, absorption correction, and peak integration. It is made of a core library written in C++ with a GUI written in Qt and a Python API. A special care was brought to design a generic enough core library for integrating easily any instrument through a simple user-defined configuration file. The project was started at the ILL, Grenoble, France in 2013 (Eric Pellegrini and Laurent Chapon) and became a collaborative project with FRMII, Munich, Germany since 2016 (Jonathan Fisher, Alexander Schober and Joachim Wuttke).

Reconstructing the 3D surface of an object of which only cross-sections are available.

Nucleic acid sequence interpretation

NUCPLOT is a program which generates schematic diagrams of protein-nucleic acid interactions. The program automatically identifies these interactions from the 3D atomic coordinates of the complex from a PDB file and generate a plot that shows them in a clear and simple manner.

For simultaneously fitting X-ray and neutron diffraction pair-distribution functions to provide optimized structural parameters

nxs is a program library of routines for calculating neutron scattering and absorption cross sections on the basis of crystal structure descriptions.
Available on request from author.

Protein crystallographic modelling program

Breaks the phase ambiguity in one-wavelength anomalous scattering (OAS) or single isomorphous replacement (SIR) (substitution) protein data. The phase problem is reduced to a sign problem once the anomalous-scatterer or the replacing-heavy-atom sites are located. Applies a direct method procedure to break the phase ambiguity intrinsic to OAS or SIR data.

Object oriented Crystallographic Library

Calculate the octahedral distortion parameters of coordinate complexes.