Posted on February 12, 2019


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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Click on the Project Tab to manage projects and samples shown at left. Make sure the data runs you want to mmanual are included in the “Pending Sets” list. How much disk space am I going to need for this?

Table of Contents

How do I start over? Most manusl the time this works, but potentially less precise than extracting the information from a pair or range or orthogonal images. How do I define the beamstop shadow and why should I do this? How do I increase the Mosaicity? See the discussion above for “how far does my data go”. Generally speaking most of the parameters that affect integration are actually on the Index tab. You can also adjust the error scales in resolution shells via the Adjust Error Model button.

Hkl000 Resolution of Diffraction Data. What should I be looking for in the charts that show up after scaling? What do the Collect, Denzo, and Scale buttons in each window do? 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.

Can you explain it?

Also, the X-ray beam intensity fluctuates with time. Why do I want to do postrefinement? What if the Peak Search picks lots of peaks in the kanual ring, or picks peaks from a second lattice? Each image file name is constructed accordingto the following template: What is the Error Scale Factor and which way should I adjust it?


Additional features on this tab are: Can I rename them? What is a site definition? The “Set Beam Position” box is active only when an image is displayed with the “Display” option. No part of this document shall be reproduced, stored in a retrieval system, or transmitted by any means, electronic, mechanical, photocopying, recording, or otherwise, without written permission from HKL Research, Inc.

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”. manhal

HKL2000 Tutorial

How do I set the path? This will bring the “HKL Main” window as shown below. Setting up Data Files. 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.

Usually optimal data collection strategy is where the highest symmetry axis of the crystal is almost parallel to the rotation axis. I’ve not yet tested to see if autoProc can process this data smoothly – you may need to pull.

The worst that can happen is that you’ll collect more data than you need. However, it is always recommended to go the “Integration” window figure below first, either by clicking on the “Integration Setup” button from the “HKL Main” window or by selecting the “Integration” menu from the menu bar on the top.

Information on how to adjust various parameters to obtain good agreement is available amnual the HKL site. 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. You will need to do one cycle of refinement, again, if you change the resolution limits. I’ll discuss strategy below – you might have noticed the “Multi” button above-right on the panel and nanual where you define the multi-run data collection strategy.

How do I start over? Waiting for image frames. What if no lattice other than primitive triclinic comes up green? How can I flip through my frames at this stage to see if they all look ok?


The computer is always left running, usually logged in, usually running the Linux side of the dual-boot setup. The new system is quite fast – moving the goniostat is one of the slower steps but typical exposure times are short seconds and readout is very fast milliseconds. Why do the bars in the mosaicity histogram get thicker or thinner? Desired maximum resolution, point group symmetry and the largest primitive cell dimension of your crystal all come into play with strategy.

These options are fully documented in the HKL manual. 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.

Scalepack’s error model expects that the Chi 2 should be 1. If some of the parameters are incorrect, it can be corrected by typing their values in the above “Main HKL window” by clicking on the “Edit Set S ” button. It looks like I can put in more frames than I actually have.

The HKL-2000 Manual

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. Strong reflections in yellow and all reflections in blue. It does not have the ability to do “remote” data collection although remote monitoring of the data is on my To Do list.

In a new editor window scroll to the end of the log file and locate the “Summary of reflection intensities and R-factors by shells” table. The blue boxes mark the individual blocks of data. What are reasonable values for the error scale factor and what if I need really high ones?