HKL-2000 Online Manual




HKL-2000 Online Manual

This manual contains information to assist you during the processing of the data with the HKL-2000 program suite. From starting guide and installation process to the step-by-step data processing procedure this book will be a valuable resource. Although this manual reflects the most current information possible, you should read the Latest News for information that may not have been available prior to our documentation being finalized.

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.

Copyright © 2007 by HKL Research, Inc.

Table of Contents



Step 1: How to start the HKL-2000 program?

How do I start?

Can I start from any directory?

What are the files that make up the HKL-2000 suite, and what do they do?

Step 2: Detector and site info

What is a site definition?

I donít see my detector listed!

How do I make a new site if mine isnít listed?

What is Goniostat Type button?

How do I verify that the site information is correct?

What if I choose the wrong site because I wasnít sure?

          What is the meaning of the goniostat alignment windows?

Step 3: Raw data source

How do I use the Directory Tree?

How do I set the path?

Canít I just type the path into the little boxes?

Step 4: Output data files

I donít see the ../proc directory. How do I make one?

Do I have to have a ../proc directory, or can I put the files anywhere?

How much disk space am I going to need for this?

Step 5: Setting up Data Files  

What am I looking at in the dialog box that comes up?

Should I click Show All Sets?

How to recover from an ambiguous name scheme?    

What if I donít see any frames listed?

Why would I want to click Scale Sets Only? 

Can I click more than one set of data?  Why would I want to do this?

Step 6: Experimental details

What if I selected a set by mistake and want to remove it?

What do the Collect, Denzo, and Scale buttons in each window do?

What if I donít want to process all of the frames in this set or I want to process some of them separately?

The Distance that came up in the Experiment Geometry window is wrong.  How do I fix it?

Frame Geometry: It looks like I can put in more frames than I actually have. What is this for?



Step 7: Display Your Image

Wow, my crystal diffracts great!  Is that the correct resolution in the green box?

How many peaks do I want to use?                                                                                     

What if the Peak Search picks lots of peaks in the ice ring, or picks peaks from a second lattice?

Can I get rid of some peaks I know shouldnít be included?

Can I add some peaks that I think the autoindex should use?

How can I flip through my frames at this stage to see if they all look ok?

Can I index on another frame?  Can I index on peaks collected from several contiguous frames?

Adjusting the display: How can I make the diffraction image look "better"? You know, darker peaks, lower background.

Step 8: Autoindexing

How do I define the beamstop shadow and why should I do this?

What does the blue highlight in the Sets Pending box mean?

Why would I want to put in any other resolution limits?

At what point should I be concerned with the Refinement Options?

Indexing keeps flashing. How long is this supposed to take?

What if there arenít any green circles? What if they donít line up on real spots?

Step 9:  Lattice parameter refinement 

Oops!  The preds donít line up with the spots anymore!

I think the direct Beam Position is wrong.  How do I change it?

What should I set at the 3D window?  

Whatís the procedure for choosing the correct lattice?

What if no lattice other than primitive triclinic comes up green?

What are the Positional and Partiality χ2 values and what should they be? What are the numbers in parentheses?

What are all those the Refinement Information values for, and what do they mean?

Someone told me to gradually increase the resolution and alternate cycles of fitting a few parameters. Why shouldnít I do this?

Step 10: New lattice refinement

Problems Ė predicted reflections donít line up with spots, things get worse, etc.

How do I start over?  How do I get back to P1?

Step 11: Resolution Limits, Fitting Radius and Spot Size

What is the Profile Fitting Radius and how do I determine what it should be?

How do I set the spot size? Is it all that important? Why do larger spots make my χ2 Ďs worse?

What is the Elongation Limit?

Resolution Limits:  should I set this here or not worry about it?

What are all these parameters Rotx, Roty, Rotz, X-beam, Y-beam, crossfire, mosaicity?

What is the Reference Zone?  How is this useful?

Step 12: 3D Window and Mosaicity

What is the 3D Window?

Why do I have to keep the 3D Window at 1 for image plate data?

What are the limitations for 3D Window usage?

Why wouldnít I just want to set the 3D Window to encompass all of my frames?

What is Mosaicity?  What does the histogram under Check Mosaicity mean?

How do I set the Mosaicity? Should I try to increase the mosaicity until all of the spots on the image are covered with preds?

How do I increase the Mosaicity?



Step 13: Integration

The Integrate Sets Button is red. Is this a problem?

The Crystal Slippage and Special Integration buttons.

What are these plots supposed to look like and how do I know if everything is ok?

What is an acceptable range for χ2?

ďHouston, weíve got problems.Ē The χ2 values are getting larger!

Why do the bars in the mosaicity histogram get thicker or thinner?

How long should this take?  How do I know if the program is stuck?

Waiting for image frames.

Once the integration is complete, should I update the site?

        How do I stop and start over?

Step 14: Scaling

Why do I want to do postrefinement?  Which one should I choose?

Scaling Options: What are Scale Restrain, B Restrain, Fix B, Ignore Overloads, etc.?

Should I change the resolution now?

What are the three Scalepack output Files? Can I rename them?  Where do they go?

Someone told me my statistics will be better if I decrease the number of zones. Should I do this?

What is the error model and should I adjust it?

How many cycles should I refine for and how do I know how to set this?

Whatís the rejection file and why am I writing it?

Step 15: Output plots and Error Scale Factor

What is the Error Scale Factor and which way should I adjust it?

What are reasonable values for the error scale factor and what if I need really high ones?

What should I be looking for in the charts that show up after scaling?

How many reflections should I be rejecting?

Whatís the difference between a reflection being marked for rejection and actually rejected?

How do I treat data that contains an anomalous signal?

Space Group Identification: How do I do this?

How to start scaling from .x files without re-integrating diffraction images.


Statistics and Scalepack.

The Resolution of Diffraction Data.

Understanding the Scalepack log file scale.log                                                              

Appendix - Installation notes