Chapter 11.4 DENZO and SCALEPACK

Crystallography of biological macromolecules

Second Online Edition (2012)

Part 11. Data processing

  1. Z. Otwinowski1,
  2. W. Minor2,
  3. D. Borek1,
  4. M. Cymborowski2

Published Online: 14 APR 2012

DOI: 10.1107/97809553602060000833

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Otwinowski, Z., Minor, W., Borek, D. and Cymborowski, M. 2012. DENZO and SCALEPACK. International Tables for Crystallography. F:11:11.4:282–295.

Author Information

  1. 1

    UT Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390–9038, USA

  2. 2

    Department of Molecular Physiology and Biological Physics, University of Virginia, 1300 Jefferson Park Avenue, Charlottesville, VA 22908, USA

Publication History

  1. Published Online: 14 APR 2012


This chapter describes the analysis of raw diffraction data, used to produce scaled and merged diffraction amplitudes. The general description of the process is provided within the context of how it is performed in the programs DENZO and SCALEPACK. The data analysis determines many parameters of the diffraction experiment that impact the quality of the final result, providing a flexible and robust approach to problems encountered by crystallographers. Topics covered include: diffraction from a perfect crystal lattice; autoindexing; coordinate systems; experimental assumptions; prediction of the diffraction pattern; detector diagnostics; multiplicative corrections (scaling); global or post refinement; and control through a graphical interface.


  • absolute configuration;
  • autoindexing;
  • coordinate systems;
  • coordinate systems in DENZO;
  • detector distortions;
  • diffraction-pattern prediction;
  • diffraction physics;
  • flood-field detector calibration;
  • indexing;
  • lattice pseudosymmetry in autoindexing;
  • lattice symmetry in autoindexing;
  • misindexing;
  • mosaicity;
  • post refinement;
  • scaling;
  • twinning