Giovanni Luca Cascarano

SIR97: a new tool for crystal structure determination and refinement

SIR97 is the integration of two programs, SIR92 and CAOS, the first devoted to the solution of crystal structures by direct methods, the second to refinement via least-squares–Fourier procedures. Several new features have been introduced in SIR97 with respect to the previous version, SIR92: greater automatization, increased efficiency of the direct methods section, and a powerful graphics interface. The program also provides publication tables and CIF files.

Completion and refinement of crystal structures with SIR92

An automatic procedure for recovering a complete crystal structure after a direct phasing process is described. The procedure consists mainly of a Fourier recycling method that can be implemented in any direct-methods package. The residual R value attained at the end of the process provides an estimate of the degree of success of the structure determination. The procedure can also be applied using a small molecular fragment as prior information. The procedure has been implemented into SIR92, the successor to SIR88.

SIR2004: an improved tool for crystal structure determination and refinement

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 A, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

SIR2002: the program

Dipartimento di Scienze della Terra Piazza UniversitaÁ, 06100 Perugia, Italy, Istituto di Cristallografia, CNR, Sezione di Monterotondo, CP 10, Monterotondo Stazione, 00016 Roma, Italy, Istituto di Cristallografia, CNR, c/o Dipartimento Geomineralogico, UniversitaÁ di Bari, Campus Universitario, Via Orabona 4, 70125 Bari, Italy, and CNR, Istituto di Cristallografia c/o Dipartimento Geomineralogico, UniversitaÁ di Bari, Campus Universitario, Via Orabona 4, 70125 Bari, Italy. Correspondence e-mail: carmelo.giacovazzo@ic.cnr.it

SIR88 – a direct-methods program for the automatic solution of crystal structures

SIR88 is an integrated package of computer programs for the solution of crystal structures. The package is based on the estimation of one- and two-phase structure seminvariants and three- and four-phase structure invariants according to the theory of representations [Giacovazzo (1977). Acta Cryst. A33, 933–944; (1980). Acta Cryst. A36, 362–372]. The program works in all the space groups and in most cases it is able to provide the correct solution without user intervention. Some prior information like the availability of a partial structure or of pseudotranslational symmetry is easily exploited to obtain the structure solution.

IL MILIONE: a suite of computer programs for crystal structure solution of proteins

IL MILIONEIl Milione is the title of the book by Marco Polo, dictated to Rustichello da Pisa in 1298 in the Genova prison where Marco was imprisoned after a naval battle between Genova and Venezia. Il Milione is a travel report: the name suggests the millions of marvels seen during the travel. Most contemporaries thought that they were a million tales. Our program is also a travel report, but in the world of crystallography. 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 A). (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: a new package for crystal structure determination and refinement

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 three-dimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.

EXPO: a program for full powder pattern decomposition and crystal structure solution

EXPO is the integration of two programs, EXTRA and SIRPOW.92, the first devoted to full powder pattern decomposition and the second to the solution and refinement of crystal structures. The program is able to exploit the prior information obtained during the crystal structure solution process for improving the classical decomposition. EXPO also allows preliminary cycles of Rietveld refinement.

E-map improvement in direct procedures

The quality of an E map is usually affected by systematic and/or random phase errors, by amplitude truncation effects in the series representation of the electron density, by the experimental uncertainty in the estimation of |E| and by the intrinsic nature of the Fourier coefficients used (i.e. the Es). It is shown that simple supplemental calculations can improve the quality of an E map. Large molecular fragments can often be localized in the new map even when the original one is not easily interpretable.

Crystal structure determination and refinement via SIR2014

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 Difference) 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.