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HKL Package

The HKL Package consists of denzo (data reduction), scalepack (guess) and xdisp (viewing frames, can be used in conjunction with denzo).
The programs are written and maintained by Wladek Minor (wladek@iwonka.med.virginia.edu) and Zbyszek Otwinowski (zbyszek@mix.swmed.edu). HKL Research, Inc has a homepage.

Hard copy documentation (by Dan Gewirth) is available in the core area for this program. It is somewhat obsolete. On-line documentation is available also.

Where and What to Find

On the Macscience and Raxis computers, a local copy of the HKL package will be found in the ./denzo directory of the user home directory. It will be included in your path, and the rx4disp, rx2disp and dipdisp aliases will be preset for you.

The HKL package is currently licensed for the following CSB computers:
SGI:texaco, chevron, exxon, adenine, darwin, bao2, taso3, sro2, rbo2, poo2, pdo2, oso2, iro2, ganesh, bigsky, bondi, csbasn, csbile, csbjoe, csbleu, csblys, csbrna, csbthr, csbtyr, csbval, macsci, raxisa and raxisb.
On SGI's the package consists of HKL2000, scalepack, scalepack8m, scalepack16m, scalepackmanyframes, scalepacknorm, xdark, denzo, denzo_3d, xdisp.
Dec Alphas: bhima, atlas, ajax, atlas and hercules.
On Dec Alphas the following is available: denzo, denzo_3d, denzobig, scalepack, scalepack8m, scalepack16m, scalepackmanyframes, scalepackvirus, xdark, xdisp
Linux: digger, emperor, pelican, puffin, saxs
Software available: HKL200, denzo, denzo_3d, scalepack, scalepack8m, scalepack16m, scalepackmanyframes, scalepackvirus, scalepacktest, xdark, xdisp

Please notify the system staff if you have problems runing the programs on any of the licensed CSB computers.

Note : HKL2000 GUI will not run on machines with memory less than 256MB.

On core computers, it can be found in /srv/local/denzo/$version/$arch/.
The current directory will point to the latest version.
However, you can most easily access the HKL package via the setup aliased command.

How to Use it

On one of the licensed hosts in the CSB Unix cluster, simply type:

setup hkl

Your path will be properly set.
type HKL2000, denzo, scalepack or xdisp
to run any of those programs.
However, there is a new syntax for the display program. The general form is:

xdisp detectortype filename

EG, you would type, xdisp dip 2000 abc001.ipf to display a file from the Macscience DIP 2000. If you simply type, xdisp, you will get a list of all formats supported.

However, the setup procedure defines aliases for you:

rx2disp -- display Raxis-II frames
rx4disp -- display Raxis-II frames (100 micron)
dipdisp -- display macscience frames
ccdadsc -- display frames from CHESS ADSC CCD
ccdsol -- display frmaes from CHESS CCD 1K

We have no tutorial for the HKL suite of programs. MSC has a tutorial designed for people using their equipment at their site. It might have some value to CSB users, but some of the commands it gives will not work or will be wrong for our environment.

Using denzo with 200- or 50-micron RAXIS4 data

To display frames collected on the RAXIS4 at 200 microns (the default is 100), use:

xdisp raxis4 200 filename...

To process the frames with denzo, use:

format raxis4 200
raster 0.2

Of course, you should substitute 50 and 0.05 for 200 and 0.2 if you have 50-micron frames [presumed but not tested].


If you think you have found a bug, or have other questions or problems, you can ask local experts (if any) and/or the program authors. If you have discovered undocumented bugs/features/folklore, please send a copy of the relevant correspondence to perlo@csb.yale.edu.


Z. Otwinowski and W. Minor "Processing of X-ray Diffraction Data Collected in Oscillation Mode", Methods in Enzymology, Volume 276: Macromolecular Crystallography, Part A, pages 307-326,  1997, C. W. Carter, Jr. & R. M. Sweet, Eds., Academic Press.

Here is a typical view of the DENZO graphical interface.

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Last Modified: Friday, 11-Jan-2002 13:20:04 EST by S. Kunchaparty