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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The scale factor was allowed to vary during this run and you can see how the scale factor changed during of data collection. At very high manuxl, you can even hkl2000 the numerical intensity values of each pixel.

Detector and site info. If the new beam position information was saved using the “Update Site” button, it is now possible to try indexing with the newly selected beam position after aborting the current refinement using “Abort Refinement” button.

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”. Parameter refinement may quite easily fall into false local minima during minimization. In this exercise you will learn how to process raw diffraction images and how to go through data reduction to a set of intensities or structure factor modules.

Since the new system has a video camera for crystal centering you can easily check on crystal status without getting anywhere near it during exposure.

By picking a space group that is compatible with the Bravais lattice you intrinsically assign a point group to the data: When a reflection is not complete on a single image is it called a partial, and continues on a the following image.

Then middle-mouse click on the Frame button at top right in XDISP to load the next image, which will also peak search and the peaks added to the list. How can I flip through my frames at this stage to see hkl22000 they all look ok? For weak data you’d probably do well to decrease the sigma cutoff for data in refinement, as given in the Refinement box in the Control panel to the right.


Peaks from a number of images for indexing can be selected by clicking hkl000 the “Frame” box of the xdisplayf window using the center mouse button before clicking “OK” for the peak search. 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 bkl2000 because it shows the predictions vs observed reflections in real time.

Running HKL at SSRL

How do I do this? An image appears in a new pop-up window. Denzo, like other refinement programs, uses learnt profile fitting to provide a better estimate of weak data by estimating weak spot profiles by generating empirical spot profiles from nearby strong spots. How does the image look? Clicking on the “More Options” button brings additional parameters for advanced spot adjustments as shown below.

Check that the data runs listed in the table at top left are all the ones you want to integrate, then press Integrate. The HKLR version of the program can be used to analyse data you’ve already collected and cannot control the machine.

If this is not the first time you’ve integrated the data you’ll be prompted if you want to overwrite the “. Under the Global Refinement section of the scale tab there’s a variety of options manusl fall under the general heading of postrefinement so named because it occurs after the data integration step, but “global” is perhaps a more informative name.

How do I make one? As with synchrotron data collections I strongly advocate checking the progress of your data collection in real time and with the Pilatus system it’s a lot closer to real time than the RAXIS system.

The HKL-2000 Manual

How do I use the Directory Tree? You want to adjust the sled that is perpendicular to the camera. If it turns out that your space group is orthorhombic and contains one or two screw axes, you may need to reindex the data to align the screw axes with the standard definition. What is the Elongation Limit? Why do I want to do manuzl Can I click more than one set of data? Strategy makes use of the unit cell, space group and crystal orientation that you’ve determined during auto-indexing.


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 hll2000 pressed while moving the window.

While one of the graphs monitor crystal mosaicity for each set of frame graph on the left side belowthe second graph can display Chi square, Cell, Crystal, mosaicity, or Distance variations during the integration process right side graph below shows Chi square variations. The very first version of this document was an extended rant on the theme of how it was unwise that the vendor ship me that pile of junk, and how equally unwise it was of the manula author name still redacted to regard it as functional.

Can I add some peaks that I think the autoindex should use? Then, click the left mouse button again to keep the window in that view. HKL will suggest the unit cells that can index the diffraction pattern in the best way green color – the lowest percentage indicate the best fit of your data and lattice. Is this a problem?

The HKL Manual | HKL Research Inc.

Inherently a number of semi-empirical parameters are refined to minimize the intensity differences between observed reflections that should have the same intensities based on symmetry. Inspect the reflection predictions on the image window in yellow.

Red reflections are ones with a problem: In this process, the program analyzes each image to locate the reflections and determine their intensities. How do I increase the Mosaicity?

HKL2000 Tutorial

During integration, HKL shows the progress of refinement with two graphs on the lower portion of the “Integration” window. Are the spots distinct or smudged. Can I add some peaks that I think the autoindex should use? If necessary, this line can be removed by selecting it with a mouse button and clicking on the “Remove Macro” box.