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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Please note that the current version of HKL doesn’t work well if you change the image number after indexing the frames. This will bring a small “Blind Region Coordinates” window with necessary information on how to define the blind region. How do I know if the program is stuck?
Strategy You will be using Rigaku’s strategy program rather than HKL3K’s own strategy program since the former is aware of the multi-axis goniostat. When a reflection is not complete on a single image is it called a partial, and continues on a the following image. By picking a space group that is compatible with the Bravais lattice you intrinsically assign a point group hml2000 the data: Inspect the reflection predictions on the image window in yellow.
To move the window up and down move the cursor to the left or right edge of the HKL window and keep the left mouse button pressed while nkl2000 the window. How do I define the beamstop shadow and why should I do this?
For some well-diffracting proteins – like the HEWL xtal here – you can actually use the very small sulphur anomalous scattering signal to determine the structure but for weakly diffracting proteins you can mostly ignore the presence of this signal. The default files for each of these detectors are available in these areas and they can be accessed by selecting the corresponding detector and clicking on Ok.
The Resolution of Diffraction Data. This box notifies the user about the status of the heavily used processors only and it can be usually ignored. Clicking on the “Simpler Options” window brings the previous simple view of the “Integration Box” window.
How do I make one? Are they very close to each other or overlapped? Someone told mxnual my statistics will be better if I decrease the number of zones. It’s not a perfect world. Why would I want to do this? What is this for? Again, you’ll have to use existing images to assess the likely limit of hkl2000 based on your current exposure time, although of course you can adjust this during the data processing step.
Select “Use rejections on next run” and hit the “Scale Set” button again.
Running HKL at SSRL
Make sure you define a Project and Crystal either via the fields in this manuaal or via the Project tab. On the top of the window is the icon bar which you can use to open a Terminal if you want to use standard Unix commands e.
If you turn on absorption correction it will additionally refine an empirical absorption correction parameterized as spherical harmonics.
Parts of the original rant may slip through the edit, or there may be new reasons to rant. Check that the data runs listed in the table at top left are all the ones you want to integrate, then press Integrate. You now need to scale the data so that all the equivalent reflection can be merged together. If you have two screw axes, then your space group is Hkl0200, with the screw axes along a and b. Under the Global Refinement section of the scale tab there’s a variety of options that fall under the general heading of postrefinement so nanual because it occurs after the hk,2000 integration step, but “global” is perhaps a more informative name.
Due to the scattering of an atom we can see how the reflection intensity decreases in higher resolutions.
Which one should I choose? The HKL system also has tools for validating the results by self-consistency checks.
Can you explain it? Is that the correct resolution in the green box? Why would I want to click Scale Sets Only?
Someone told me to gradually increase the resolution and alternate cycles of fitting a few parameters. This window gives access to different programs Indexing, Integration.