HKL 2000

SER-CAT Computing Resources

Any publication arising from use of the HKL program package should contain the following reference:

Z. Otwinowski and W. Minor, "Processing of X-ray Diffraction Data Colledt in Oscillation Mode", Methods in Enzymology, Volume 276: Macromolecular Crystallography, part A, p.307-326, 1997, C.W. Carter, Fr. &R.M. Sweet, Eds., Academic Press (New York).

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HKL-2000 HKL-2000 is a new program package based on extended versions of Denzo, Xdisplayf and Scalepack. It consists of several more subprograms coordinated by the graphical command center. The most important new elements are: strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc.

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HKL-2000 The software is driven by the graphical user interface, which greatly improves convenience of working with various data sets.

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	HKL-2000 A Primer

	Data processing with HKL2000 HKL2000 is a unified data processing package which brings together Denzo, Xdisplayf, Scalepack and other programs using a graphical interface. This introduction assumes you will run the program from the data directory, but any directory created by the user may also be used. On starting the program with the command hkl2000 the main control window appears:

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HKL-2000 Site Configuration File

All commands, from reading in image files to scaling datasets, are performed using the menus in this interface. The MAR165 CCD Site Specific Configuration file is located in: /usr/local/hklint/Mar165/def.site Please remember, you will need a copy of the Site Specific Configuration file for processing data frames collected at SER-CAT and processed at the home laboratory using HKL2000 This file establishes parameters specific to the detector at the PX station being used:

	Images are read by clicking on Set Up Data Files in the file information box. This will open a small window with your data files...

...it automatically sets the working directory path names for input and output (these may be edited if necessary, e.g. to create a directory for .x files). For this demonstration a single 'high' resolution run data set of 123 images is selected (highlighted in red); it is possible to select more than one dataset at a time. Press Add Set and then the Select button in the Main window. The file template for processing the images is now set and information about the images are displayed:

	The Summary menu gives an overview of the dataset and parameters used in further data processing (e.g. box size in Denzo). These may be viewed in the summary table by clicking a box in the View Controls panel:

		The next step is to go to the Index/Refinement/Integration window:

	In the Controls panel select Display to open the Xdisplayf window:

Press Peak Search in the Xdisplayf window (or in the hkl2000 GUI) to store peak information for Denzo and then click on the Index button in the Controls menu. Denzo produces its standard list of possible unit cells (in this case primitive rhombohedral is the most probable solution):

Click OK to accept this solution, close the window and click on Refine in the Controls panel to begin refinement. By default 5 cycles of refinement are performed on the parameters highlighted in the Refinement options panel. Further parameters can be included in refinement by clicking on the relevant item or by clicking on Fit All (or switched off using Fix All). The output of the refinement process is produced in the Refinement information panel...

The Scaling menu window provides options for scaling and post-refinement using Scalepack:

...and by a summary of the scaling and postrefinement statistics:

The Controls window provides options for displaying information (e.g. Show Redundancies) or for editing scaling parameters( e.g. Adjust Error Model):

 

Home Page. http://www.hkl-xray.com/ HKL2000 Manual. http:www.HKL-xray.com/hkl/manual_online.pdf