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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Why would I want to put in any other resolution limits? An image appears in a new pop-up window. How do I do this?
Data Collection are the sort of parameters you’d use if you actually want to collect an entire dataset.
Primary assigned Space Groups. The “” gets automatically incremented, starting at 1, when you collect images. Note that hkk2000 cannot do any better than this i. The most useful part of the Align sub-tab is the Crystal Mount option that drives the goniostat to the appropriate position to mount and remove your crystal. If you have one screw axis, your space mahual should be P, with the screw axis along c.
What manial this for? This offset information can be given to the program by entering the new beam center in the “Site Configuration” window.
Index the data and refine the parameters using the Index Tab in exactly the same way I outlined above. Should I do this? What does the blue highlight in the Sets Pending box mean?
If you have two screw axes, then your space group is P, with the screw axes along a and b. How many cycles should I refine for and how do I know how to set this? This whole analysis assumes that you have a crystal of an enantiomorphic compound, such as protein, where only proper symmetry proper rotation is possible.
If you’re unhappy with the spot predictions and wish to discard the current parameters you’ll need to press the Abort Refinement button to go back and do peak searching or indexing again. The Resolution of Diffraction Data. Can I rename them? 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 moving the window. Sets of images for further processing can be selected or deselected by clicking on the corresponding sets.
Click on Zoom In a few times to, well, zoom in. Check again the correspondence between predicted and observed spot centroids. The files you want from the processing directory are output. How long is this supposed to take? Remember to tighten the grub screw on the phi axis once your crystal is centered.
Please note that this box will become active only when an image is displayed with the “Display” option. For actual data collection use the Data Collection button which has many of the same parameters as Crystal Check. In reality things aren’t quite that clean, since anisotropic scattering will turn up in part in the per-frame B-factor, and longer-term variations in e. The “Integration Information” panel at lower right will show you positional chi 2unit cell parameters etc during integration.
How do I set the Mosaicity? Values hk2l000 green required relatively little distortion and those in red require more distortion and are unlikely to be correct. If you selected 2 or 3 data sets e. During integration, HKL shows the progress of refinement with two graphs on the lower portion of the “Integration” window.
Mwnual do I get back to P1? To remove irrelevant data runs, press Select in the hkl20000 box and then Remove Set in the Set Controls panel.
The HKL Manual | HKL Research Inc.
Selections are not possible on a zoomed window. It is possible to add spots from more than one contiguous set of images. There are some behind-the-scenes analytical corrections for Lorentz and polarization factors, air absorption etc but then Scalepack refines a per-frame scale factor k and a per-frame B-factor B as a primary method of reducing systematic differences in the data – i.
Can I start from any directory?
Table of Contents
During this period, the “xdisplayf” window will also updated and show changes representing the indexing process. The Scaling program can be selected by clicking on the “Scaling” box from the top menu of any “HKL window”. Due to the scattering of an atom we can see how the reflection intensity decreases in higher resolutions.
The check boxes below-left control what parameters you want to refine to improve predicted and observed spot positions, and a few things about spot size.
What should I be looking for in the charts that show up after hkl20000 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 are the files that make up the HKL suite, and what do they do? Click on each tab to reach the function for each.
What is the Reference Zone? It consists of three parts: Optimally, you should choose the highest symmetry lattice with a low distortion parameter. How do I use the Directory Tree? When a reflection is not complete on a single image is it called a partial, and continues on a the following image.