General Information


The HKL (HKL-2000) suite of programs is designed to analyze monochromatic X-ray diffraction oscillation data. The programs have been written by Dr. Zbyszek Otwinowski (Southwestern Medical Center, University of Texas) and Dr. Wladek Minor (University of Virginia). By seamlessly incorporating other crystallographic software packages, the HKL-3000 suite allows users to perform all crystallographic steps (data collection, integration, scaling, structure determination, model building, model refinement, and structure validation) using the HKL interface. A database module is available for HKL-3000 that tracks crystallographic progress for an unlimited number of projects. The HKL suite uses the following programs:

  •  DENZO - Auto-indexing, refinement
  •  XDISPLAYF - Image display and measurement
  •  SCALEPACK - Data scaling
  •  STRAT - Strategy (HKL-2000)
  •  CDIR_T - disk manipulation tools (HKL-2000)
  •  HKLINT - Command Center and GUI user interface (HKL-2000)
  •  XDARK - dark current calculation (HKL-2000)
  •  SHELXC, SHELXD, and SHELXE - Phasing (HKL-3000)
  •  MLPHARE - Heavy atom refinement (HKL-3000)
  •  MOLREP - Molecular Replacement (HKL-3000)
  •  DM - Density Modification (HKL-3000)
  •  POINTLESS - Spacegroup verification (HKL-3000)
  •  ARP/WARP - Model building and solvent placement (HKL-3000)
  •  BUCCANEER - Model building (HKL-3000)
  •  SOLVE/RESOLVE - Model building and NCS detection (HKL-3000)
  •  PROFESS - NCS detection (HKL-3000)
  •  COOT - Model Manipulation (HKL-3000)
  •  REFMAC5 - Strucure Refinement (HKL-3000)
  •  MOLPROBITY - Model Validation (HKL-3000)

The HKL suite development is supported by the NIH grant GM-53163 to the laboratories of Zbyszek Otwinowski (Southwestern Medical Center at Dallas) and Wladek Minor (University of Virginia). Grant GM-53163 funds HKL package development but does not fund general program distribution or user support (solving individual problems).

The HKL program package is available at many synchrotron beamlines.

Availability for users of synchrotron beamlines

US academic and non-commercial institutions

Experimenters that perform non-commercial research may freely use the program for data evaluation and processing, while collecting data at the beamline. These experimenters can also obtain a temporary, free of charge, license to (re)process data collected at synchrotron beamlines. This license can be obtained by contacting HKL Research, Inc.

Commercial institutions and commercial research

Experimenters from commercial and for-profit institutions or researchers that would like to use the program for commercial research must have an appropriate commercial HKL license.

Availability at synchrotron beamlines

1. NIH funded synchrotron beamlines

All NIH funded beamlines can obtain a non-commercial license for the developmental version, free of any license charges. The license can be obtained through a letter which requests the license and identifies the beamline and funding sources.

2. DOE and NSF funded synchrotron beamlines

All federally funded beamlines can obtain a license for the developmental version on the basis of scientific collaboration, free of any charges. The terms of scientific collaboration can be established by a letter stating the conditions of such a collaboration.

3. US beamlines with access controlled by competition based on scientific merit

All US open beamlines can obtain a license on the basis of scientific collaboration. The scientific collaboration can be established by a letter stating the conditions of such a collaboration. The license is free of charge. The program is regularly updated, so the copies are time stamped and usually are upgraded every 3-6 months. The authors intend that this time period will grow to one year as the program code matures and stabilizes.

4. Other US non-commercial beamlines

Non-commercial beamlines may enter into a collaborative agreement with the program authors' laboratories and obtain a free of charge program license, or they may obtain an academic license from HKL Research, Inc.

5. Commercial and non-US beamlines

Commercial and non-US beamlines may obtain a license from HKL Research, Inc.

6. Other

If the beamline does not have a license and the user has a license under the terms as specified above, the user may use the program on the user's computer or may process the data at home.

New Instruments

Beamlines that belong to categories 1-3 may request a generic version of the program, which will handle an input data format with requested frame size (in pixels) and pixel dimensions. The data model will assume a flat or cylindrical detector and will assume a linear scale for the data intensities.

HKL-3000 upload server

HKL-3000 upload server


Use of the package should be referenced in publications as follows:

Z. Otwinowski and W. Minor "Processing of X-ray Diffraction Data Collected in Oscillation Mode", Methods in Enzymology, Volume 276: Macromolecular Crystallography, part A, p. 307-326, 1997, C.W. Carter, Jr. and R.M. Sweet, Eds., Academic Press. [View HTML document]


Source Code

The source code is available for inspection and discussion in the program authors' laboratories.


The HKL Manual is available on-line.


  • Otwinowski Z, Minor W  (1997)
    Processing of X-ray diffraction data collected in oscillation mode.
    Methods in Enzymology 276: 307-326.  Times cited: 30061.  

  • Otwinowski Z, Minor W  (2001)
    Denzo and Scalepack.
    International Tables For Crystallography, Volume F F: 226-235.  

  • Minor W, Tomchick DR, Otwinowski Z  (2000)
    Strategies for macromolecular synchrotron crystallography.
    Structure Fold Des 8: R105-10.  Times cited: 62.  [Pub Med ID: 10801499]

  • Minor W, Otwinowski Z  (1996)
    Advances in Accuracy and Automation of Data Collection and Processing.
    Proceedings Of IUCr Computing School  Bellingham, 1996