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WinLALS for a linked-atom least-square refinement program for helical polymers on windows PCs. (English) Zbl 1049.92042

Summary: Fiber diffraction data from polymers are sufficiently different in kind and quantity from single crystal data as to warrant analyses with a different emphasis: refinement of competing molecular models where torsion angles and bond angles are the explicit variables rather than atomic coordinates. The first linked-atom least-squares (LALS) refinement program had been devolved at Arnott’s laboratories at King’s College, London on mainframes and several revised versions were maintained at Purdue University on workstations. Today the LALS users have to choose correctly any one program that they want to use, trigonometric or Bessel functions, from some versions.
To develop a new WinLALS program based on the dimensioned version of the latest LALS2000 program, we reviewed all the mathematical expressions and corrected the optimization of the non-bonded atomic contact terms. The WinLALS is coded with FORTRAN90 and runs on MICROSOFT-WINDOWS PCs and the many amendments including changing input/output assignments, expanding array sizes, arranging that the update files have all output parameters of each cycle, and correcting several bugs, are performed.
This paper describes the mathematical expressions in detail employed in WinLALS and compares results of its applications obtained with those obtained earlier.

MSC:

92E10 Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
92-04 Software, source code, etc. for problems pertaining to biology
92-08 Computational methods for problems pertaining to biology
82D60 Statistical mechanics of polymers

Software:

WinLALS
PDFBibTeX XMLCite
Full Text: DOI

References:

[1] Alden, C. J.; Arnott, S., Nucleic Acids Res., 2, 10, 1701 (1975)
[2] Arnott, S., Fiber diffraction analysis of biopolymer molecules, Trans. Am. Crystallogr. Assoc., 9, 31 (1973)
[3] Arnott, S.; Wonacott, A. J., Polymer, 7, 157 (1966)
[4] Arnott, S.; Wonacott, A. J., J. Mol. Biol., 21, 371 (1966)
[5] Arnott, S.; Scott, W. E., J. Chem. Soc. Perkin Trans., 2, 324 (1972)
[6] Arnott, S.; Chandrasekaran, R.; Selsing, E., (Sundaralingam, M.; Rao, S. T., Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions (1975), University Park Press: University Park Press Baltimore, Maryland), 577-595
[7] Chandrasekaran, R. 2000. lals; Chandrasekaran, R. 2000. lals
[8] Chandrasekaran, R.; Balasubramanian, R., Biochim. Biophys. Acta, 188, 1 (1969)
[9] Chatani, Y.; Hasegawa, Y.; Tadikoro, H., Polym. Prep. Jpn., 20, 420 (1971), Japanese
[10] Cochran, W.; Crick, F. H.C.; Vand, V., Acta Crystallogr., 5, 581 (1952)
[11] Compaq fortran; Compaq fortran
[12] Cruickshank, D. W.J., (Computing Methods and the Phase Problem in X-ray Crystal Analysis (1961), Pergamon: Pergamon Oxford), 32-78
[13] Ichikawa, Y.; Suzuki, J.; Washiyama, J.; Moteki, Y.; Noguchi, K.; Okuyama, K., Polymer, 35, 15, 3338 (1994)
[14] Ichikawa, Y.; Kondo, H.; Igarashi, Y.; Noguchi, K.; Okuyama, K.; Washiyama, J., Polymer, 41, 4719 (2000)
[15] Lagridge, R.; Marvin, D. A.; Seeds, W. E.; Wilson, H. R.; Hooper, C. W.; Wilkins, M. H.F.; Hamilton, L. D., J. Mol. Biol., 2, 38 (1960)
[16] Naya, S.; Nitta, I., A note on the derivation of structure factors of helical polymers, Kwansei Gakuin Univ. Ann. Studies, 15, 1 (1966)
[17] Obata, Y.; Okuyama, K.; Kurihara, S.; Kitano, Y.; Jinda, T., Macromolecules, 28, 1547 (1995)
[18] Okada, K.; Okada, S., X-Ray crystallographic analysis and semiempirical computations, (Schleyer, P.v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F.; Schreiner, P. R., The Encyclopedia of Computational Chemistry (1998), Wiley: Wiley Chichester, UK), 3223-3247
[19] Okada, S.; Okada, K., Z. Kristallogr., 215, 131 (2000)
[20] Okada, S.; Okada, K., Comput. Chem., 24, 143 (2000)
[21] Okuyama, K.; Obata, Y.; Noguchi, K.; Ito, Y.; Ohno, S., Biopolymers, 38, 557 (1996)
[22] Okuyama, K.; Noguchi, K.; Miyazawa, T.; Yui, T.; Ogawa, K., Macromolecules, 30, 5849 (1997)
[23] Okuyama, K.; Noguchi, K.; Hanafusa, Y.; Osawa, K.; Ogawa, K., Biol. Macromol., 26, 285 (1999)
[24] Rollett, J. S., Least-squares procedures in crystal structure analysis, (Ahmed, F. R., Crystallographic Computing (1970), Munksgaard: Munksgaard Copenhagen), 167-184
[25] Smith, P. J.C.; Arnott, S., Acta Crystallogr. Sect. A, 34, 3 (1978)
[26] Smith, P.J.C., Chandrasekaran, R., 1983. lals; Smith, P.J.C., Chandrasekaran, R., 1983. lals
[27] SPARCworks Professional fortran; SPARCworks Professional fortran
[28] Tadokoro, H., Structures of Crystalline Polymers (1976), Kagaku-Dojin Publishing: Kagaku-Dojin Publishing Kyoto, Japan, Japanese
[29] Tadokoro, H., (Robert, E., Structures of Crystalline Polymers (1990), Krieger: Krieger Mallabar, FL, USA)
[30] Tanaka, S.; Naya, S., J. Phys. Soc. Jpn., 26, 982 (1969)
[31] Wilson, A. J.C., Nature, 150, 151 (1942)
[32] Yui, T.; Imada, K.; Okuyama, K.; Obata, Y.; Suzuki, K.; Ogawa, K., Macromolecules, 27, 7601 (1994)
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