HKL-2000 Overview

The general workflow of HKL Select the detector used to collect the data. Select the data and results directories. Display and Peak Search the data to find reflections. Auto-index the data in all crystal classes and select the best guess. Index the data in the selected crystal class (assign Miller Indices). Integrate the data. This indexes each image, refines relevant parameters, and combines partial reflections for each set of consecutive images. Integration generates *.x files, which contain Miller Indices, intensities, and errors for every recorded reflection. Scale the data. In simplistic terms, this ensures that the data is merged together properly with respect to image to image variations, and that symmetrically equivalent reflections are merged properly. Analyze the data. HKL presents many informative graphs that let you instantly know the quality of your data.
There is a logical path from raw X-ray diffraction images to a crystal structure, and HKL aims to guide you through these steps. The default settings have been selected to work well for most cases, and the manual has been designed to emphasize the most critical parameters that you should pay attention to. A Quick Start document is available on the HKL Research web site that can guide you through data processing with example data.

 

The HKL-2000 Tabs

The next few pages show the layout of the different tabs in HKL-2000, briefly describe the tasks performed on each tab, and provide information about where in the manual to look for more detailed information.

The Project Tab

Figure 1. The Project tab contains information about the macromolecule. Using this tab, you can load or save session information, including which data sets to work with. Some of the features in the Project tab are more useful in database linked versions of HKL-2000 and in all versions of HKL-3000, which requires a database module license. See Create, Save, and Load Projects on page 36 and The Project Tab After Scaling on page 119.

 

The Data Tab

Figure 2. The Data tab displays information about input and output files, displays information about individual datasets, and has control buttons to work with the datasets. The top of this tab shows the datasets that you are working with and what you intend to do with them. The middle of the page allows you to load and edit the sets you want to use, and the lower part of the display gives information about the currently selected set. See Data, Results, and Datasets starting on page 25.

 

The Auto Tab

Figure 3. The Auto tab provides you with one-click processing and scaling your data. See Automatic Data Processing starting on page 121.

 

The Summary Tab

Figure 4. The Summary tab provides detailed information about your datasets and refinement parameters. Parameters that vary from set to set are highlighted in cyan. The selector buttons can be used to change which information is displayed in the table. In this case, these two sets have been collected using the same strategy, but at different wavelengths. See Checking and Editing Sets on page 32.

The Index Tab

Figure 5. The Index tab allows you to index your data and refine various parameters. This tab also includes buttons to mask the beamstop and specify the beam center. In this figure, the refinement has been completed, and this data is ready to be integrated. The left side of the display contains control buttons and parameters. The top right shows indexing statistics and crystal characteristics. The bottom right contains action control buttons and a few more parameters. See Auto-Indexing starting on page 52.

 

The Strategy Tab

 

Figure 6. The Strategy tab can help you design your data collection experiment. An optimal initial orientation will give you a complete dataset before collecting redundant data, thereby minimizing complications due to crystal decay. Simulating a run will let you know if you should expect overlapping reflection, which can severely degrade the quality of your data. See Strategy and Simulation on page 77.

 

The Integrate Tab

Figure 7. The Integrate tab updates while processing the individual frames. Refinement information and mosaicity distribution for each frame are shown along with a graph of how refinement parameters change over the course of the dataset. See Integrating on page 84.

 

The Scale Tab

Figure 8. The Scale tab is where you combine all the information from the individual frames into one Scalepack file (called output_manual.sca in this case), which contains a unique list of all reflections. Symmetry related reflections have been merged. The top panel is a scrollable selection of graphs that provide information about the data quality. The bottom pane lets you control various parameters or let you inspect results that are not initially displayed. See Scaling on page 90.

 

 

 

The Merge Tab

Figure 9. The Merge tab can be used to scale and merge multiple individually scaled data sets. This allows you to merge data from different crystals or data that could not otherwise be scaled together. See Merging Multiple Scaled Files on page 124.

 

The Macros Tab

Figure 10. The Macros tab allows you to give specific commands to HKL during various parts of data processing. The "error positional" macro is one of the more commonly used macros. It can significantly lower your positional chi2 by allowing more "wiggle room" for your reflections. This is often a detector dependent necessity. See Using Macros on page 126.

Conventions Used in This Manual

The most critical steps and information that should not be overlooked are bold, blue, and underlined.

 

HKL-2000 buttons are in a blue, small caps font.

 

File names and paths are in a fixed-width font similar to a Linux console.

 

Tabs and Options are bold and italic.

Deeper Information Some explanations and details are contained in text boxes like this one. Read the heading to decide if you need to read the information in the box.