Software: Denzo/HKL
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The DENZO/HKL 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). The HKL suite consists of the following programs:
- DENZO - Auto-indexing, refinement and integration
- XDISPLAYF - Image display and measurement
- SCALEPACK - Data scaling
The HKL package development is supported by the NIH grant GM-53163 to the laboratories of Prof. Zbyszek Otwinowski (Southwestern Medical Center at Dallas) and Prof. Wladek Minor (University of Virginia). The HKL program package available at the BIOCARS beam lines at APS is provided on the basis of scientific collaboration free of any charges by the program authors. The synchrotron versions are time stamped and are usually upgraded every 3-6 months.
Denzo/Scalepack/Xdisp (version 1.97) software (www.hkl-xray.com) is available on both the SGI's and the Linux boxes and can be executed from any prompt.
Sample input files (*.inp) are located in the /usr/local/hkl directory.
You can also view them with the links below.
HKL2000 is also available.
Xdisp and Denzo
To start the xdisp program, type
xdisp {file_format} {file_name}
For example, when using the MAR345 detector operating at the default mode, type.
xdisp mar345 345mm 100 marpck {file_name}
Here is a table of some commonly used file formats:
| Detector | File format | Input files (for denzo) |
|---|---|---|
| Quantum-1 | ccd adsc single | q1_index.inp q1_integrate.inp |
| Quantum-4 | ccd adsc unsupported-q4 | q4_index.inp q4_integrate.inp |
| Mar345 | mar345 345mm 100 marpck (for mode 4 only; Check the other modes.) | mar345_index.inp mar345_integrate.inp |
| Marccd165 | ccd unsupported-m165 | marccd_index.inp marccd_integrate.inp |
| Quantum-315 | ccd unsupported-q315 binned ccd unsupported-q315 |
q315_index.inp q315_integrate.inp |
Scalepack
The names for the different versions of scalepack have changed in version 1.96. More details can be obtained from the HKL Research web site. Please note that scalepackvirus does not work on the SGI.
Documentation
The HKL Manual, Edition 5 (September, 1998), available at the beamline. Also available are: the on-line (PDF) version of the manual and searchable lists of Denzo and Scalepack keywords.
Reference
The use of the package should be referenced in publication 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.