HKL-package general description

HKL-package is a set of programs  Denzo, XDisplayF and Scalepack  designed for monocrystal X-ray diffraction data analysis. Most crystallographic structures deposited to RCSB Protein Data Bank (nearly 80%) solved with using the data obtained with  Denzo/Scalepack  programs.

Key features of HKL-package

 • Automatic indexing
 • Positional refinement based on partially recorded reflections for high accuracy and computational stability
 • Flexible, weighted, profile fitting algorithm for accurate measuring of the intensity of the diffraction spots
 • Visualization of the data in the original form as well as the progress of data reduction
 • Scaling and merging of different data sets and global refinement of crystal parameters

Hardware and OS requirement for HKL-package

This program suite distributed as already compiled executable files and supported operational systems are:
 • Linux (RedHat 9.0, RedHat Enterprise, Fedora Core, Altix SGI Enterprise)
 • SGI Irix 6.5
 • OSF 3.2, but this OS is not supported now and the last available version of  HKL / HKL2000  for OSF is 1.97.9 / 0.97.647d
 • IBM AIX Unix


For proper operation the minimal hardware requirements are:  Memory  - 512 Mb,  Swap Space  - 1.5Gb.

HKL-package reference

Any publications, mentioned HKL-package, should contain the following reference:

Otwinowski Z. and Minor W.,
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. & R. M. Sweet, Eds.,

Programs for Protein Crystallography

- Protein crystallography
Main steps:
- Protein purification
- Crystallisation
Special:
- Programs for crystallography
- ADSC-software
- HKL package
- HKL2000 package
- HKL2MAP
- Pocket
- X-ray detectors
Basic tutorials:
- Chemistry
- Protein
- Peptide
- Amino Acids
Xtal community:
- CCP4BB

 
It is impossible to imagine modern X-ray Protein Crystallography without wide set of program tools for almost all X-ray data manipulations. For standard studies you do not need to write your own programs, it is much easier and faster to look through manuals and find what is more suitable for required calculations.

Programs for protein crystallography written by different group of scientist are different in the strategy of they usage. Some of them have a very smart GUI-interface and make life much easier in simple cases, but carefully hide some important parameters make them almost unchangeable. Other programs require writing a very long command files with using of special language for this. Some programs are exist as a single command file to run, when others contains a waste number of small executable files for all cases.

Here we've try to make a complete list of all known programs for Protein Crystallography, but if you know some useful programs which is not in the list - please send us a message about this and we will be very happy to improve our list.
Data collection
ADSC-software - Developed by ADSC as CCD control software. Distributed with any Quantum CCD detectors.
Data processing and reduction
HKL-package - Designed and developed by Dr. Wladek Minor and Dr. Zbyszek Otwinowski for single crystal X-ray diffraction data processing.
Denzo
XDisplayF (xdisp)
Scalepack
HKL2000-package - Designed and developed by Dr. Wladek Minor and Dr. Zbyszek Otwinowski for single crystal X-ray diffraction data processing. This program suite can be considered as a further development of HKL-package.
Denzo
XDisplayF (xdisp)
Scalepack
Strat
Cdir_T
HKLINT
Structure solution
SHELX
HKL2MAP
Protein analysis
POCKET - program for drawing active site of an enzyme.