Structure

Laboratory of Macromolecular Crystallography



This is a review of the works carried out in LMC of the IMPB RAS. Information on other papers in this field may be found in the original papers listed below.

Development of crystallographic software

(1979-2002)

       The development and support of crystallographic software is a main activity of LMC, and it was the very first work related to protein crystallography, which was carried out at the Institute in the late 70's. The first crystallographic packages adopted to available at that time computers were those developed by L.Ten Eyck for solution of the phase problem by Multiple Isomorphous Replacement method and for calculation of Fast Fourier Transform [1-2]. It is worthy of noting that for those years it was not a simple problem and it required essential efforts of both programmers and computer-managing staff.

       The next software project was concerned with the problem of atomic model refinement. This work started with adaptation of the refinement program developed by R.Agarwal. This program was based on the most advanced (for those years) ideas and, in particular, included an effective algorithm for calculation of structure factors and the gradient of discrepancy between calculated and observed magnitudes of structure factors. Nevertheless, this program did not allow one to control strereochemical parameters of the model during the process of refinement. Therefore in actual practice an additional program was requited which could restore a correct model geometry [4]. To avoid this problem the laboratory started a project aimed at creating a new program, which would offer both efficient computing algorithms and a possibility to include geometry restraints into the criterion to be minimized. This project was not completed due to an unexpected event. It was Dr. K.Kim's talk at an annual conference of the Research Computing Centre, which was held at the beginning of 1983 in Pushchino. The main idea of the talk was that for any function (which could depend on any number of variables) an algorithm may be constructed, which would enable one to calculate all the components of the function gradient for the same time as is required to calculate one function value. (This fact was understood independently by two groups - a group consisted of K.Kim, Yu.Nesterov and B.Cherkassky, and the one consisted of W.Baur and V.Strassen). After this talk it became clear that an ingenious algorithm suggested by Agarwal is a particular case of some general idea and that an equally efficient algorithm of the gradient calculation may be created for any refinement criterion. This resulted in the development of a general approach to the construction of refinement programs, which was used as the basis for a refinement program FROG [3, 5-11, 17, 19]. The program FROG provided a user with a lot of non-standard (for that time) possibilities and had high speed of calculations. In particular it enabled the work with models of viruses on very weak computers [12]. Unfortunately, this work was stopped in the laboratory in early 90's.

       With the advent of cheap personal computers, the laboratory got some fresh opportunities for visualising studied objects and, in particular, density distributions. Unfortunately, this potential was not supported at that moment by crystallographic software. To overcome this impediment we developed some program tools for calculating and analysing Fourier syntheses on PC [13-16]. Though the programs were initially designed for AT 286 computers, they still provide a convenient tool for some stages of low-resolution studies.

       Some results concerning the development of crystallographic software were summed up in E.Vernoslova's PhD thesis [20-21].

       In late 90's the development of interactive software with a Tcl/Tk based interface was started [25-27].

       These notes provide some historical sketch, but they do not cover all the software developed in the laboratory. Usually, the development of all laboratory projects was followed by devising of relevant programs.

March, 24, 2003
V.Lunin

Publications

The full texts of papers

  1. Lunin, V.Yu. (1979). "The program package FFT". Software, FORTRAN, 3, NCBI AN SSSR, Pushchino, Russia. (In Russian)

  2. Lunin, V.Yu. (1979). "The phasing program of L.ten-Eyck". Software, FORTRAN, 4, NCBI AN SSSR, Pushchino, Russia. (In Russian)

  3. Lunin, V.Yu. (1982). "Optimization of calculation of structure factors in protein crystallography". Preprint, NCBI AN SSSR, Pushchino, Russia. (In Russian)

  4. Kuzin, A.P. & Urzhumtsev, A.G. (1983). "LSQ-refinement of actinoxanthin structure at 1.8A resolution". All-Union Symp. on Chemistry of Proteins and Peptides, Riga, 1983, Coll. Abstr., 186. (In Russian)

  5. Lunin, V.Yu. & Urzhumtsev, A.G. (1983). "Program construction for macromolecular atomic model refinement based on Fast Fourier and Fast Differentiation algorithms". Preprint, NCBI AN SSSR, Pushchino. (In Russian)

  6. Lunin, V.Yu. & Urzhumtsev, A.G. (1985). "Program construction for macromolecule atomic model refinement based on the fast Fourier transform and fast differentiation algorithms". Acta Cryst., A41, 327-333.

  7. Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1988). "Program package FROG". Software, FORTRAN, 10, NCBI AN SSSR, Pushchino, Russia. (In Russian)

  8. Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1989). "The program complex FROG for local refinement of atomic structures of macromolecules". In Computing methods of protein engineering, Software, Institute of Mathematics AS BSSR & Institute of biochemistry, 86, 86-97, Minsk. (In Russian).

  9. Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1989). "FROG - high-speed restraint-constraint refinement program for macromolecular structure". J.Appl.Cryst., 22, 500-506.

  10. Urzhumtsev, A.G., Lunin, V.Yu. & Vernoslova, E.A. (1990). "New refinement program FROG gives new possibilities to study macromolecular models". Proc.of the First Intern. Meeting on Structure and Chemistry of Ribonucleases, Moscow, USSR, December 1989, 410-415.

  11. Urzhumtsev, A.G. (1991). "How to calculate planarity restraints". Acta Cryst. A47, 723-727.

  12. Morgunova, E.Yu., Mikhailov, A.M., Urzhumtsev, A.G. & Vainstein, B.K. (1992). "Crystal structure of the CMtV capsid at 6A resolution". Kristallografiya, 37, 2, 396-404. (In Russian)

  13. Vernoslova, E. & Lunin, V. (1992). "FAN Scalar Field Analysis", Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 27, 35.

  14. Vernoslova, E. (1992). "FFT Discrete Three-Dimensional Fourier transform". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 27, 36.

  15. Vernoslova, E. & Lunin, V. (1992). "CAN Comparative Analysis of three-dimensional Functions". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 27, 37.

  16. Vernoslova, E.A. & Lunin, V.Yu. (1993). "The FROG PC series: programs for electron-density and model investigation for proteins", J.Appl.Cryst., 26, 291-294.

  17. Vernoslova, E.A. & Urzhumtsev, A.G. (1994). "Current development in the program package FROG for atomic model refinement". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 30, 27-28.

  18. Urzhumtsev, A.G. & Podjarny, A.D. (1994). "Programs for translation searches with two independent models simultaneously". J.Appl.Cryst., 27, 122-124.

  19. Ivanov, M.E. & Urzhumtsev, A.G. (1995). "FROG PC - a menu-based environment for atomic model refinement program on a personal computer". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, 20-22.

  20. Vernoslova, E.A. (1996). "The development and the use of software for the protein crystallography purposes". Resume of Ph.D.Theses, ONTI PNC RAN, Pushchino, Russia. (In Russian)

  21. Vernoslova, E.A. (1996). "The development and the use of software for the protein crystallography purposes". Ph.D.Theses, Institute of Crystallography RAS, Moscow, Russia. (In Russian)

  22. Urzhumtsev, A.G. (1996). "Relations between some rotation descriptions for molecular replacement procedure". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 32b, 43-46.

  23. Urzhumtseva, L.M. & Urzhumtsev, A.G. (1996). "Tcl/Tk-based programs. I. CONFOR - user-friendly converter for crystallographic data files". Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 32b, 40-42.

  24. Urzhumtsev, A.G., Skovoroda, T.P. & Lunin, V.Yu. (1996). "A procedure compatible with X-PLOR for the calculation of electron-density maps weighted using an R-free-likelihood-based approach". J.Appl.Cryst., 29, 741-744.

  25. Urzhumtseva, L.M. & Urzhumtsev, A.G. (1997). "Tcl/Tk-based programs. II. CONVROT: a program to recalculate different rotation descriptions". J.Appl.Cryst., 30, 402-410.

  26. Urzhumtseva, L.M. & Urzhumtsev, A.G. (1998). "Programs Tcl/Tk based crystallographic software : current state and new programs". CCP4 Newsletter on Protein Crystallography, 35, 22-24.

  27. Urzhumtseva, L.M. & Urzhumtsev, A.G. (1999). "Tcl/Tk based programs. III. CRITXPL: graphical analysis of the X-PLOR refinement log-files". J.Appl. Cryst., 32, 376-377.