JANA2006 is a freely available program for structure determination of standard, modulated and magnetic samples based on X-ray or neutron single crystal/ powder diffraction or on electron diffraction. The system has been developed for 30 years from specialized tool for refinement of modulated structures to a universal program covering standard as well as advanced crystallography. The aim of this article is to describe the basic features of JANA2006 and explain its scope and philosophy. It will also serve as a basis for future publications detailing tools and methods of JANA.

The recently published method for the structure refinement from threedimensional precession electron diffraction data using dynamical diffraction theory [Palatinus et al. (2015). Acta Cryst. A71, 235-244] has been applied to a set of experimental data sets from five different samples -Ni 2 Si, PrVO 3 , kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å . The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.

Accurate structure refinement from electron-diffraction data is not possible without taking the dynamical-diffraction effects into account. A complete three-dimensional model of the structure can be obtained only from a sufficiently complete three-dimensional data set. In this work a method is presented for crystal structure refinement from the data obtained by electron diffraction tomography, possibly combined with precession electron diffraction. The principle of the method is identical to that used in X-ray crystallography: data are collected in a series of small tilt steps around a rotation axis, then intensities are integrated and the structure is optimized by least-squares refinement against the integrated intensities. In the dynamical theory of diffraction, the reflection intensities exhibit a complicated relationship to the orientation and thickness of the crystal as well as to structure factors of other reflections. This complication requires the introduction of several special parameters in the procedure. The method was implemented in the freely available crystallographic computing system Jana2006.

We report a new structure determination of the Sr1.2872NiO3 incommensurate composite hexagonal perovskite compound. Three different refinement strategies are presented:  (i) a 3D supercell approximation with a nonharmonic development of the atomic displacement factor, (ii) an original (3+1)D incommensurate composite description with the use of crenel functions, and (iii) a (3+1)D commensurate composite model. The three strategies are discussed and compared to previous refinements carried out for the hexagonal perovskites in a classical way or with the superspace group formalism. Out of the three methods, the incommensurate composite approach gives slightly better results with a final global R value of 2.89% for 635 independent reflections (at a I/σ(I) > 2 level) and only 60 parameters (R3̄m(00γ)0s superspace group; a = 9.5177(7) Å, c = 2.5739(2) Å, q = 0.64359(4)c*, V = 201.93(4) Å3, and Z = 3). The use of crenel functions notably improves previously reported results. New structural features are evidenced for Sr1.2872NiO3:  (i) an incommensurate character, (ii) a splitting of the trigonal prismatic nickel atoms over 5 positions, (iii) a definite stoichiometry which induces a perfect charge balance, and (iv) a nonharmonic behavior of some Sr atoms. Those characteristics seem general to most hexagonal perovskite compounds and essential for correctly interpreting their interesting magnetic properties. Finally, a new generic formulation is proposed, which explains the various stoichiometries observed and suggests a new compound possibility.