Skip to main content

A Statistical Potential for Modelling X-ray Electron Density Maps with Known Phases

  • Chapter
Maximum Entropy and Bayesian Methods

Part of the book series: Fundamental Theories of Physics ((FTPH,volume 36))

Abstract

We describe methods for constructing a Maximum Entropy X-ray electron density map in crystallography that fits certain amplitudes and phases uniquely subject to a squared residual constraint. The calculations use a free energy analogue, or statistical potential that derives from the grand partition function of the maximum entropy problem in Fourier space. It is a function of the statistical forces, the Lagrangian multipliers of the entropy. Three new functions Y, G and Ψ allow us to fit the data with predetermined accuracy, and to avoid divergences which would otherwise occur. The method is able to handle physically realistic and elaborate models: cells with fixed density regions, several types of scattering atom, anomalous dispersion. The control algorithm, and the relation between the domains of the force and probability variables are outlined.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Gull, S.F. & Danieli, G.J. (1978). Nature 272, 686–690.

    Article  Google Scholar 

  2. Skilling, J. & Bryan, R.K. (1984). Mon. Not. R. Astron. Soc. 211, 111–124.

    MATH  Google Scholar 

  3. Skilling, J. & Gull, S.F. (1985). In Maximum-Entropy and Bayesian Methods in Inverse Problems. Ed. C. Ray Smith & W.T. Grandy. pp. 83–132. Dordrecht Holland: Reidei Publishing Company.

    Chapter  Google Scholar 

  4. Livesey, A.J. & Skilling, J. (1985). Acta Cryst. A41, 113–122.

    Google Scholar 

  5. Skilling, J. (1986) In Maximum Entropy and Bayesian Methods in Applied Statistics. Ed. James H. Justice. Cambridge: University Press. pp. 156–193.

    Chapter  Google Scholar 

  6. Collins, D.M. (1982). Nature 298, 49–51.

    Article  Google Scholar 

  7. Gull, S.F., Livesey, A.K. & Sivia, D.S. (1987). Acta Cryst. A43, 112–117.

    Google Scholar 

  8. Wilkins, S.W., Varghese, J.N. & Lehmann, M.S. (1983). Acta Cryst. A39, 47–60.

    MathSciNet  Google Scholar 

  9. Wilkins, S.W. (1983). Acta Cryst. A39, 892–896.

    MathSciNet  Google Scholar 

  10. Wilkins, S.W. (1983). Acta Cryst. A39, 896–898.

    MathSciNet  Google Scholar 

  11. Navaza, J. (1985). Acta Cryst. A41, 232–244.

    Google Scholar 

  12. Navaza, J. (1986). Acta Cryst. A42, 212–223.

    Google Scholar 

  13. Bricogne, G. (1984). Acta Cryst. A40, 410–445.

    Google Scholar 

  14. McLachlan, A.D. (1987). Gazzetta Chimica Italiana 117, 11–15.

    Google Scholar 

  15. Luenberger, D.G. (1984). Linear and Non-linear Programming. 2nd Edition. Reading Mass: Addison-Wesley Publishing Co.

    Google Scholar 

  16. Gill,P.E.,Murray, W.& Wright, M.M.(1981). Practical Optimisation.New York:Academic Press.

    Google Scholar 

  17. Levine, R.D. (1976). J. Chem. Phys. 65, 3302–3315.

    Article  Google Scholar 

  18. Levine, R.D. (1986) In Maximum Entropy and Bayesian Methods in Applied Statistics. Ed. James H. Justice. Cambridge: University Press. pp.59–84.

    Chapter  Google Scholar 

  19. Bryan, R.K., Bansal, M., Folkhard, W., Nave, C. & Marvin, D.A.(1983). Proc. Nat. Acad. Sci. USA 80, 4728–4736.

    Article  Google Scholar 

  20. Bryan, R.K. & Banner, D.W. (1987). Acta Cryst. A43, 556–564.

    Google Scholar 

  21. Bricogne, G. (1988). Acta Cryst. A44, 517–544.

    MathSciNet  Google Scholar 

  22. Wang, B.C. (1985). In Methods in Enzymology, Vol 114. Diffraction Methods in Biological Macromolecules. Ed. H.W. Wyckoff, C.H.W. Hirs & S.N. Timasheff, pp. 114–167. New York: Academic Press.

    Google Scholar 

  23. Prince, E., Sjölin, L. & Alenljung, R. (1988). Acta Cryst. A44, 216–222.

    Google Scholar 

  24. Podjamy, A.D., Moras, D., Navaza, J. & Alzari, P.M. (1988). Acta Cryst. A44, 545–550.

    Google Scholar 

  25. Marvin, D.A., Bryan, R.K. & Nave, C. (1987). J. Mol. Biol. 193, 315–343.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1989 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

McLachlan, A.D. (1989). A Statistical Potential for Modelling X-ray Electron Density Maps with Known Phases. In: Skilling, J. (eds) Maximum Entropy and Bayesian Methods. Fundamental Theories of Physics, vol 36. Springer, Dordrecht. https://doi.org/10.1007/978-94-015-7860-8_23

Download citation

  • DOI: https://doi.org/10.1007/978-94-015-7860-8_23

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-90-481-4044-2

  • Online ISBN: 978-94-015-7860-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics