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 initial quality of that software was relatively poor with several functional bugs including one or two dangerous ones. 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 author author name still redacted to regard it as functional. Parts of the original rant may slip through the edit, or there may be new reasons to rant. Controlling the Machine The control computer is dual boot – one side of it is a Centos Linux operating system running HKLR to control the machine and the flip side is a Windows 7 operating system running CrysAlis Pro.

This document doesn’t cover CrysAlis Pro – look elsewhere for that.

HKLR effectively controls the goniostat and detector, indexes data, calculates strategy and processes the data. The name of the control computer is mol-xray3. It does not have other user accounts other than those used for data collection. It does not have the ability to do “remote” data collection although remote monitoring of the data is on my To Do list. 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 useful because it shows the predictions vs observed reflections in real time.

HKLR is very closely related to the data processing in HKL – in fact the data processing parts are essentially identical. CBASS used for this.

Rigaku Strategy program – present in the previous version, using it is now essential since there’s more than one axis to consider. Upon login, the default Desktop has icons for the software on the left-hand side. The HKLR version of the program can be used to analyse data you’ve already collected and cannot control the machine. Other icons of interest are XGControl for controlling the generator, ImageViewer which is apparently Rigaku’s image viewing program, and a standalone version of the Rigaku Strategy program – probably not a lot of use without importing Denzo’s idea of crystal and goniostat parameters.

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. That’s the icon right next to the System menu. The web browser Firefox is the icon next to that. Phenix are likely to be added in the near future. Quit any existing instances of HKLR to avoid accidentally overwrite other people’s data. Click on each tab to reach the function for each.

If you’re screening crystals you’ll just use Project and Collect. If you’re collecting data or want to auto-index your data you will use more of the tabs further to the right. If you’ve used HKL then the general layout is hll2000. 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.

Manjal the Project and Crystal framework to keep images for each protein under a distinct project name, with different crystals being a new crystal within a project. Avoid making names absurdly long. Click on the Project Tab to manage projects and samples shown at left. You can create new projects, save existing ones, load old ones. When HKL starts it defaults to a generic project name – it doesn’t save your old project info so you should remember to save it manually mwnual quitting and load it after starting.


It’s possible to collect data manuap process it without changing the default project name. Just make sure you specify a separate and unique data directory name for your data and processing directories.

I generally recommend against doing this if you’re actually collecting data since kanual makes more sense to cluster related datasets into one project. To reload an existing project, use the Load button within the Project tab and locate the relevant. An alternative to this interface is to use the Project, Crystal and Base Directory fields in the Collect tab.

The “” gets automatically incremented, starting at 1, when you collect images. You can use the Data Directory field in the Collect tab to provide a different directory structure e. Here’s what you see if you click on the New Project button. The main reason to enter it is if you plan on using HKLR to solve your structurefor you not covered here where the sequence is useful for finding homologs or calculating the expected number of sulphurs.

Most of the options on the project screen are a waste of time for the simple purpose of crystal screening. Nevertheless it’s a good idea to use New Project and New Crystal to manage subdirectories and filenames – or the equivalent fields in hkl200 Collect tab – since the facility manager is very likely to delete generic “project1” files if the disk starts to fill up.

The Collect is by far hkl20000 most important tab. To start doing something productive you should mount your crystal and click on the Collect Tab which brings up what you see at left.

The buttons on the left are the important ones. You need to press the Connect button to manul the program to talk to the machine – this establishes connections to the servers in the generator itself.

It also initializes the detector and all axes on the goniostat khl2000 it does so – this takes a while since the goniostat isn’t all that fast. Below the Connect button the radio buttons select what type of experiment you’re doing. Crystal Check loads default parameters for the sort of images we shoot to test crystals. Data Collection are the sort nkl2000 parameters you’d use if you actually want to collect an entire dataset. We’ll come back to those settings, below.

Make sure you define a Project and Crystal either via the fields in this tab or via the Project tab. The screen shot at left is from the Collect sub-tab within the Collect tab yes, that’s confusing but there are two other tabs within Collect that are useful: This is the Align tab within Collect.

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. You cannot adjust the centering from here. The most useful part of the Align sub-tab is the Crystal Mount option that drives the goniostat to the appropriate position to mount mmanual remove your crystal.

Manuak centering your crystal be aware that for best results you need to point a gkl2000 sled toward the camera and not toward you. You want to adjust the sled that is perpendicular to the camera. Takes a little while to adjust to if you’re used to the former optical microscope being right in front of you. If manuzl crystal is moving weirdly on centering check that you’re doing this. The goniostat has no vertical adjustment on the phi axis, but there is a certain amount of vertical travel on the goniometer head.

Be sure to mount your empty loop before starting the experiment to make sure the height is approximately correct and your pin length will work on this setup. The standard length of 21mm sometimes called 18mm pin length will work just fine. Remember to tighten the manyal screw on mqnual phi axis once your crystal is centered. This is the Manual tab within Collect.

If you want manuxl drive to a specific goniostat amnual, this is where you’d enter it. The current limits on goniostat angles are: Generally speaking be ultra-cautious about driving the goniostat into positions manually – drive them perhaps half-way and visually check for potential collisions.


Now, back to the Collect sub-tab within Collect. Data Collection loads the sort of parameters you’d use if you actually want to collect an entire dataset. Once you’ve changed the values the blue button at left marked Collect Sets will be enabled and you can collect the images. The new system is quite fast – moving the goniostat is one of the slower steps but typical exposure times are short hkl20000 and readout is very fast milliseconds. For actual data collection use the Data Collection button which has many of the same parameters as Crystal Check.

Running HKL at SSRL

I’ll discuss strategy below – you might have noticed the “Multi” button above-right on the panel manyal that’s where you define the multi-run data collection strategy. Additional features on this tab are: The Status button is sometimes a more reliable source of information. 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 mwnual clicking for a living.

Since I’m both a Luddite and a Curmudgeon you’ll frequently find me muttering while reading the actual logs rather than the pretty little graphs. The rotation axis on the kanual source is vertical i.

It’s usable to 1. Desired maximum resolution, point group symmetry and the largest primitive cell dimension of your crystal all come into play with strategy.

I recommend adding 0. Usually optimal data collection strategy is where the highest symmetry axis of the crystal is almost parallel to the rotation axis. However with the module boundaries being horizontal – perpendicular to the rotation axis – this might give rise to systematic discs of missing data – and this is likely to be more pronounced in low symmetry space groups at lower resolutions. 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.

Indexing and Generating a 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.

In the Data tab HKL will load all data runs associated with the project – both test images and data collection runs, and also for data runs that are about to be collected. The blue boxes mark the individual blocks mnaual data. To remove irrelevant data runs, press Select in the blue box and then Remove Set in the Set Controls panel. The red check buttons within each blue data run block offer control whether the data is scheduled to be integrated and scaled.

Also when processing data mannual collecting test oscillations, make sure you deselect those test frames since they add nothing to the data.

HKL2000 Tutorial

Majual collection parameters for the selected data set are shown at the bottom of the tab. Normally the correct number is found automatically, but you can use this to exclude ranges of frames hk2000 the start or end of a set from processing. Indexing your diffraction pattern is a necessary precursor to strategy calculation – symmetry axis orientations need to be known. Go to the Index tab – verify that the data frame s listed are the ones you want to index via the panel at top left – adjust via the Data Tab.

The buttons below-right control the workflow within Index. The check boxes below-left control what parameters you want to refine to improve manuxl and observed spot positions, and a few things about spot size.

Most of the time this works, but potentially less precise than extracting the information from a pair or range or orthogonal images.