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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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It looks like I can put in more frames than I actually have.

How do I set the path? Make sure you define a Project and Crystal either via the fields in this tab or via the Project tab. What is the Reference Zone? Generally speaking be ultra-cautious about driving the goniostat into positions manually – drive them perhaps half-way and visually check for potential collisions.

Sets of images for further processing can be selected or deselected by clicking on the corresponding sets. HKL also has an option to execute “user created” macros during any of the data processing steps.

Using HKL for Data Collection at Princeton University

First we have to display an image and perform a “peak search” operation. What are the three Scalepack output Files? Clicking on the “Simpler Options” window brings the previous simple view of the “Integration Box” window.

Most of the steps in data processing are analogous to my HKL Data Processing Guide which was written inprior to the era in which y’all have been reduced to button clicking for a living. Please note that this box will become active only when an image is displayed with the “Display” option.

The Status button is sometimes a more reliable source of information. Clicking on the “More Options” button brings additional parameters for advanced spot mqnual as shown below. In a new editor window scroll to the end hk2000 the log file and locate the “Summary of reflection intensities and R-factors by shells” table. Usually the HKL program is started either from the data collection directory or from a “process” sub directory under the data collection directory.


When centering your crystal be aware that for best results you need to point a translation sled toward the camera and not toward you. I don’t necessarily agree with all of those decisions either, but it gets me pretty close to the desired end-point without me having to click any buttons. The basic subset of the parameters selected by default is a good way to start refinement. The Integrate Sets Button is red.

The HKL-2000 Manual

Wow, my crystal diffracts great! But the second table from the top – “Global Statistics” – is a pretty good summary: CBASS used for this.

Indexing and Generating janual Strategy You can process your data while it is being collected – recommended – or you can process it later using the HKLR program icon this version doesn’t control the hardware. Indexing of the data to figure out the Laue class, Bravais lattice and cell dimensions. What is the Elongation Limit?

Data collection parameters for the selected data set are shown at the bottom of the tab. The initial quality of that software was relatively poor with several functional bugs including one hk2000 two dangerous ones. This will save the newly typed information for the current session of hml2000 program. Now you are ready to integrate the data. Here’s what you see if you click on the New Project button. Waiting for image frames. To get a look at the spot size, first ykl2000 on Zoom Wind button in XDISP to open the zoom window, then middle-mouse click somewhere on the master image to center the view in the zoom window.


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.

How do I use the Directory Tree? Which one should I choose? While the highest symmetry choice is hol2000 the best one – for HEWL the point group is with a primitive lattice so primitive tetragonal is indeed the correct choice – a minority of crystals show pseudo-symmetry and the correct assignment of point group and unit cell dimensions only becomes obvious during scaling. The goniostat has no vertical adjustment on the phi axis, but there is a certain amount of vertical travel on the goniometer head.

What if no lattice other than primitive triclinic comes up green? Also when processing data after collecting test oscillations, make sure you deselect those test frames since they add nothing to the data. What is an acceptable range for Chi2? In the Data tab HKL will load all manal runs associated with the project – both test images and data collection runs, and also for data runs that are about to be collected.

Why do I have to keep the 3D Window at 1 for image plate data? How to recover from an ambiguous name scheme? The central one is controlled by the Spot Size parameter in the index tab. Denzo presents this table of possible indexings in the “Bravais Lattice Table”. The reflection position in 2D spacethe intensity, and background will be stored in a working directory as a series of files with the extension. You cannot adjust the centering from here.

Should I click Show All Sets?