This manual contains information to assist you during the processing of the data with the HKL program suite. From starting guide and installation process. The information provided in this site is specific for running HKL at SSRL. The HKL on-line manual is available at the HKL Research. HKL Online Manual. Your diffraction data. In this exercise you will be working with an X-ray diffraction data set collected for a single crystal of trypsin at .

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An alternative to this interface is to use the Project, Crystal and Base Directory fields in the Collect tab.

Click on the Project Tab to manage projects and samples shown at left. The Status button is sometimes a more reliable source of information. When HKL starts it defaults to a generic project name – it doesn’t save your old project info hkl200 you should remember mnual save it manually before quitting and load it after starting.

The primary space groups are the first space groups in each Bravais lattice type in the table below. Denzo writes a file with extension “.

How do I set the spot size? How do I use the Directory Tree? Leave Use Rejections on Next Run unchecked. I think the direct Beam Position is wrong.

Click Rigaku Strategy to launch the program. Remember to tighten the grub screw on the phi axis once your crystal is centered. Postrefinement – activated if you select anything above the bottom option – considers the manhal of diffraction maxima on all the frames at once, so in particular it should provide much more accurate unit cell dimensions for downstream use.

Due to the scattering of an atom we can see how the reflection intensity decreases in higher resolutions. A general view of the “Scaling window” before running scaling program is shown below.

The HKL-2000 Manual

What do the Collect, Denzo, and Scale buttons in each window do? Comparison with HKL You might have encountered HKL at the synchrotron – in some cases it’s used as the default method to process data and can be useful because it shows the predictions vs observed reflections in real time.


In the Zoom window you should be able to see the individual pixels of the detector, each with its own degree of blackness, proportional to the number of X-ray quanta accumulated during the exposure.

How to start the HKL program?

It’s not a perfect world. But the second table from the top – “Global Statistics” – is a pretty good summary: How do I define the beamstop shadow and why should I do this? By picking a space group that is compatible with the Bravais lattice you intrinsically assign a point group to the data: Manuap color-coding is by redundancy this data is overkill – there’s nearly always mahual separation and the explanation for the scheme is via the Explanation button, as it is for most graphs.

How long should this take? The Integrate Sets Button is red.

HKL2000 Tutorial

The new beam position information can be either applied to the current refinement by selecting “Apply Current” or it can be entered into the Site Configuration window by selecting “Update Site”. Recall that during indexing and during integration the refinement of parameters – particularly unit cell dimensions – the refinement is quite local and doesn’t consider the whole of diffraction space. The per-frame correction factors model things that vary primarily with image number, of which primary absorption and scattering effects due to the variation of the volume of the crystal in the beam are the main one, and a B-factor term that potentially models the impact of radiation damage on the crystal fall-off in scattering with respect to resolution.

Generally speaking be ultra-cautious about driving the goniostat into positions manually – drive them perhaps half-way and visually check for potential collisions. It’ll take a few seconds to do this and then the GUI will parse the Scalepack log file and populate the graphs in the upper selection of the scale tab with a summary of the Scalepack log file.

Denzo presents this table of possible indexings in the “Bravais Lattice Table”. You will need to do one cycle of refinement, again, if you change the resolution limits. Normally the correct number is found automatically, but you can use this to exclude ranges of frames at the start or end of a set from processing. Can I index on another frame?


If manuao of the parameters are incorrect, it can be corrected by typing their values in the above “Main HKL window” by clicking on the “Edit Set S ” button. HKLR is very closely related to the data processing in HKL – in fact the data processing parts are essentially identical. This window allows to make changes in the integration script by clicking on the “Special Integration” box or to account for “Crystal Slippage” by clicking on the “Crystal Slippage” box.

What if no lattice other than primitive triclinic comes up green? In the Data tab HKL will load all data runs associated with the project – both test images and data collection runs, and also for data runs that are about to be collected.

Scaling Scaling your data is where you start to find out what your intrinsic data quality is, so we need to define this: What hkll2000 the Peak Search picks lots of peaks in the ice ring, or picks peaks from a second lattice?

The Resolution of Diffraction Data.

Using HKL for Data Collection at Princeton University

This will include that command on the macro area below. Scalepack is the maunal that does the scaling. In any event, all scaling methods involve exploiting the redundancy in your data as a method for estimating the quality of the scaling result is going to improve as the redundancy of your data improves. How to start the HKL program? This whole analysis assumes that you have a crystal of an enantiomorphic compound, such as protein, where only proper symmetry proper rotation is possible.

Where do they go? How many cycles should I refine for and how do I know how to set this?

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