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:
All commands, from reading in image files to scaling datasets, are performed using the menus in this inteface. First, you must Load Site Info in the Site Configuration window. Currently, this information is located in the file /usr/people/ccduser/HKL2000/SRS9.5-ADSC-corr/def.site. This will set parameters specific to 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...
...and 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...
... and is also output to the denzo.log file in the output directory.Once refinement is complete click on the Integrate Sets button and all images selected will be processed and the output files (.x files) will be written, ready for scaling. The predicted diffraction patterns for each of the images during this process may be observed by keeping the Xdisplayf window open and using the zoom button. Information about the integration process is written to the denzo.log file and to the graphical interface:
The Scaling menu window provides options for scaling and postrefinement using Scalepack:
After selecting the desired options click on Scale Sets to begin scaling the data. Information about this process is saved in scaleui.log file and is presented in several graphs in the graphical interface, together with a corresponding explanation...
...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):
