SIR2004 is the evolution of the SIR2002 program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003). J. Appl. Cryst.36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented in SIR2004 make this program efficient: it is able to solve ab initio both small/medium‐size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 Å, and to provide interpretable electron density maps. A powerful user‐friendly graphical interface is provided.

SIR2014 is the latest program of the SIR suite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, both ab initio (standard or modern direct methods, Patterson techniques, Vive la Différence) and non-ab initio (simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density maps via suitable viewers.

IL MILIONE is a suite of computer programs devoted to protein crystal structure determination by X‐ray crystallography. It may be used in the following key activities. (a) Ab initio phasing, via Patterson or direct methods. The program may succeed even with structures with up to 6000 non‐H atoms in the asymmetric unit, provided that atomic resolution is available, and with data at quasi‐atomic resolution (1.4–1.5 Å). (b) Single or multiple isomorphous replacement, single‐ or multiple‐wavelength anomalous diffraction, and single or multiple isomorphous replacement with anomalous scattering techniques. In the first step the program finds the heavy‐atom/anomalous scatterer substructure, then automatically uses the above information to phase protein reflections. Phase extension and refinement are performed by electron density modification techniques. (c) Molecular replacement. The orientation and the location of the protein molecules are found via reciprocal space methods. Phase extension and refinement are performed by electron density modification techniques. All the programs integrated into IL MILIONE are controlled by means of a user‐friendly graphical user interface, which is used to input data and to monitor intermediate and final results by means of real‐time updated messages, diagrams and histograms.

SIR2011, the successor of SIR2004, is the latest program of the SIR suite. It can solve ab initio crystal structures of small-and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities: e.g. a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometry via simulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes threedimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.

EXPO2004 is the updated version of the EXPO program [Altomare et al. (1999). J. Appl. Cryst. 32, 339–340]. The traditional steps of the ab initio powder solution process are performed automatically: indexing, space‐group determination, decomposition of the pattern for extracting the observed structure‐factor moduli, structure solution by direct methods, model refinement by Rietveld technique. Special strategies may be applied to improve both the estimates of the extracted structure‐factor moduli and the quality of the structure model. In addition, the use of special procedures exploiting available supplementary information on molecular geometry can be successfully adopted. The graphical interface has also been improved.

Ribosome-inactivating proteins (RIPs) are EC3.2.32.22 N-glycosidases that recognize a universally conserved stem-loop structure in 23S/25S/28S rRNA, depurinating a single adenine (A4324 in rat) and irreversibly blocking protein translation, leading finally to cell death of intoxicated mammalian cells. Ricin, the plant RIP prototype that comprises a catalytic A subunit linked to a galactose-binding lectin B subunit to allow cell surface binding and toxin entry in most mammalian cells, shows a potency in the picomolar range. The most promising way to exploit plant RIPs as weapons against cancer cells is either by designing molecules in which the toxic domains are linked to selective tumor targeting domains or directly delivered as suicide genes for cancer gene therapy. Here, we will provide a comprehensive picture of plant RIPs and discuss successful designs and features of chimeric molecules having therapeutic potential.

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RootProf is a multi-purpose program which implements multivariate analysis of unidimensional profiles. Series of measurements, performed on related samples or on the same sample by varying some external stimulus, are analysed to find trends in data, classify them and extract quantitative information. Qualitative analysis is performed by using principal component analysis or correlation analysis. In both cases the data set is projected in a latent variable space, where a clustering algorithm classifies data points. Group separation is quantified by statistical tools. Quantitative phase analysis of a series of profiles is implemented by whole-profile fitting or by an unfolding procedure, and relies on a variety of pre-processing methods. Supervised quantitative analysis can be applied, provided a priori information on some samples is provided. RootProf can be applied to measurements from different techniques, which can be combined by means of a covariance analysis. A specific analysis for powder diffraction data allows estimation of the average size of crystal domains. RootProf borrows its graphics and data analysis capabilities from the Root framework, developed for high-energy physics experiments.