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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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.
Table of Contents
It’s not all that uncommon for one or more parameters to drift during integration since the initial indexing h,l2000 done of one frame and the parameters are refined locally off one or a very small number of frames – they aren’t estimated mqnual a large angular range. If you’ve done any prior scaling click the “Delete Reject File” button and then at the top left of the button array in Controls, click Scale Sets.
You also need enough data for the analysis of systematic absences. If you’ve got the parameters refined so that the predicted spot centroids match reality, you’ve selected the correct Bravais lattice, and you’ve tweaked the spot size parameters as necessary you’re pretty much good to start integration.
Sets of images for further processing can hkl200 selected or deselected by clicking on the corresponding sets. Can you see the shadow of the x-ray beam stop?
Indexing of the data to figure out the Laue class, Bravais lattice and cell maual. Compare this list with the listing of reflection conditions by each of the candidate space groups. You might have to incline the symmetry axis more, and this is where the strategy program comes in, and where the partial 4-axis goniostat is of assistance.
This will bring up a small “Beam Position” window with detailed informations on how to select the beam position by clicking on a displayed image.
How many peaks do I want to use? Avoid making names absurdly long. What are the three Scalepack output Files? Is this a problem?
HKL is not an Expert System In the previous version of this document Hkk2000 waxed lyrical about the ways that HKLR could have done it better – my major axes-to-grind are Profile Fitting Radius and Spot Size and how they should be automatically adjusted, but you can go check that out for yourself.
This plots indicates the partiality of the reflections on an image, and indicated by an arrow the expected rotation in degrees required to record a full reflection. Clicking on the “Simpler Options” window brings the previous simple view of the “Integration Box” window.
If the images were collected in the “binned” mode, the binned mode button in the “Other Options” section should be selected. Click Calculate Strategy to get the program to come up with nanual.
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.
Should I click Show all Files?
Note that you h,l2000 do any better than this i. The red check buttons within each blue data run block offer control whether the data is scheduled to be integrated and scaled. Why would I want to click Scalepack Files Only?
Yellow centroid markers are partial reflections – reflections that are clipped at one or both ends of their profile during the frame and whose diffraction intensity is spread over multiple frames. How do I make one? Waiting for image frames. HKL is a data processing program that uses the underlying programs Denzo and Scalepack, and HKLR is an extension of that program to control the machine as well as process the data.
Low resolution vs completeness: Autoindexing and Amnual Refinement.
The HKL Manual | HKL Research Inc.
This window gives access to different programs Indexing, Integration. Here you can see some disjoint behavior for the last few runs 20 hlk2000 each, so 5 degrees and you might be tempted to omit them from scaling – at the bottom there’s a button for Exclude Frames to allow you to omit some especially troublesome frames, but in this case you’d just go back to the Data tab and deselect the Scale checkbox for any runs you want to delete in their entireity.
With weaker diffractors and troublesome auto-indexing situations you want to click on the Peak Sear button and pick more or less reflections than the default.
Below the Connect button the radio buttons select what type of experiment you’re doing. In this process, the program analyzes each image to locate the reflections and determine their intensities. Data Collection are the sort of parameters you’d use if you actually want to collect an entire dataset. The exception is primitive hexagonal, where you should try P61 after failing P and P If you’ve used HKL then the general layout is familiar. Appendix – Installation notes.
The per-frame correction factors model things that vary primarily with image number, of which primary absorption and scattering effects manula 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.