Computational Chemistry
Software YellowPages

SIR

A. ALTOMARE, G. CASCARANO, C. GIACOVAZZO, A. GUAGLIARDI Istituto di Ricerca per lo Sviluppo di Metodologie Cristallografiche CNR, c/o Dipartimento Geomineralogico, Campus Universitario, 70124 Bari, Italy,

M.C. BURLA, G. POLIDORI Dipartimento di Scienze della Terra, Universita', 06100 Perugia, Italy,

M. CAMALLI Ist. di Strutturistica Chimica "G. Giacomello", CNR, Via Salaria Km 29,200, 00016 Monterotondo stazione (Roma), Italy.

THE CRYSTALLOGRAPHIC PROBLEM: Our recent developments in direct methods theory and in crystal structure refinement persuaded us to develop a fully automated structure-determination program which is able to solve the phase problem and to refine atomic parameters in a single computer run.

METHOD OF SOLUTION: The method for the automatic structure determination is based on the representation theory (Giacovazzo, 1977, 1980). 1-phase structure seminvariants and 3-phase structure invariants are estimated via their second representation, 2-phase seminvariants and 4-phase invariants via their first representation. SIR92 is the heir of SIR88 (Burla, Camalli, Cascarano, Giacovazzo, Polidori, Spagna & Viterbo, 1989) of which it retains most of the features (f.e., treatment of pseudotranslational symmetry, use of prior information, tangent weighting schemes, etc.). In SIR88 1-,2-phase seminvariants and positive estimated 3-phase invariants could be actively used in the phasing process. Negative estimated triplet and quartet invariants were used as a FOM together with psi-zero triplets. In SIR92 negative estimated triplet and quartet invariants and psi-zero triplets are actively used in the phasing process, which proved to be much more robust and efficient. The various trial solutions can be obtained either by magic integer permutation (Main, 1978) or by random phases (Baggio, Woolfson, Declercq & Germain, 1978). The best trial solution, selected by powerful FOM's, is automatically processed through a cyclic procedure combining structure factor calculation - least squares - 2Fo-Fc Fourier synthesis. The final outcome is a set of refined atomic parameters (x,y,z and isotropic B values) associated with suitable atomic species. The residual R value is calculated for user usefulness (final values usually between 0.08 and 0.15). The program runs in default when supplied with a minimum amount of information (space group symbol, cell parameters, unit cell chemical content and reflections) but documentation has been produced to allow the user to change default values. If a graphic device is available the user can follow structure solution and refinement on the screen. In the final stage a menu-driven interface is available in order to study molecular geometry and restart refinement.

SOFTWARE ENVIRONMENT: The program has been written in standard Fortran77. A module written in C language is supplied in order to interface the program with X-window or DEC-Window terminals for graphics. Therefore, besides the C compiler, an Xlib library is also needed. Two ASCII files are associated to the program: the first contains coefficients for calculating scattering factors, the second, necessary for graphics, contains on-line help.

HARDWARE ENVIRONMENT: The program runs on UNIX and DEC workstations, on mainframe and on personal computers (for this last one 4 Mbytes of RAM and a VGA monitor are needed).

PROGRAM SPECIFICATION: The source code of the program consists of 41.000 FORTRAN lines and of 2000 C lines (including comments).

DOCUMENTATION: Users instructions and program description (about 1500 lines) are supplied as an ASCII text file.

AVAILABILITY: The program is available free of charge from the teams in Bari and in Perugia. A licence agreement has to be signed.

Contact info

To obtain a copy please contact Dr Cascarano providing your ftp address.

Dr. Gianluca Cascarano
Istituto di Ricerca per lo Sviluppo di Metodologie
Cristallografiche CNR
c/o Dipartimento Geomineralogico
Campus Universitario
70124 Bari, Italy
Tel: +39-80-242624
FAX: +39-80-242591
E-mail: cryst@arba.ba.cnr.it

REFERENCES

Burla, M.C., Camalli, M., Cascarano, G., Giacovazzo, C., Polidori, G., Spagna, R. & Viterbo, D. (1989). J. Appl. Cryst. 22,389-393.

Baggio, R., Woolfson, M.M., Declercq, J.P. & Germain, G. (1978). Acta Cryst. A34, 883-892.

Giacovazzo, C. (1977). Acta Cryst. A33, 933-944.

Giacovazzo, C. (1980). Acta Cryst. A36, 362-372.

Main, P. (1978). Acta Cryst. A34, 31-38.



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