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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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.

Structure of This Book. Starting the Program and Setting the Data Sets. How to start the HKL program? How do I start? Can I start from any directory? What are the files that make up the HKL suite, and what do they do?

The HKL-2000 Manual

Detector and site info. What is a site definition? What is Goniostat Type button? How do I verify that the site information is correct? How do I use the Directory Tree? How do I set the path? How do I make one? Do I have to have a. How hll2000 disk space am I going to need for this? Setting up Data Files. What am I looking at in the dialog box that comes up? Should I click Show all Files? How to recover hkl200 an ambiguous name scheme?

What if the frame numbering looks different than I had it? Why would I want to click Scalepack Files Only? Can I click more than one set of data?


Why would I want to do this? What if I selected gkl2000 set by mistake and want to remove it? What do the Collect, Denzo, and Scale buttons in each window do? What if I want to process some of the frames in this set separately?

The Distance that came up in the Experiment Geometry window hk,2000 wrong. How do I fix it? It looks like I can put in more frames than I actually have. What is this for? Autoindexing and Cell Refinement. 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 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?

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 Mabual How long is this supposed to take?

I think the direct Beam Position is wrong. How do I change it? What should I set at the 3D window? What if no lattice other than primitive triclinic comes up green?

What are the Positional and Partiality Chi2 values and what should they be? What are all those the Refinement Information values for, and what do they mean? How do I start manuql How do I get back to P1?

What is the Profile Fitting Radius and how do I determine what it should be? How do I set the spot size? What is the Elongation Limit? What is the Reference Zone? How is this useful? 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? What does the histogram under Check Mosaicity mean? How do I set the Mosaicity?

How do I increase the Mosaicity? How do I stop and start over? Indexing, Integration and Scaling the Data.

The Integrate Sets Button is red. Is this a problem? The Special Integration and Cryst. What are these plots supposed to look like and how do I know if everything is ok?

What is an acceptable range for Chi2? Why maanual the bars in the mosaicity histogram get thicker or thinner?

How long should this take? How do I know if the program is hkkl2000 Waiting for image frames. Once the integration is complete, should I update the site?

Using HKL for Data Collection at Princeton University

Why do I want to do postrefinement? Which one should I choose? 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. 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? 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 hkl20000 really high ones? What should I be looking for in the charts that show up after scaling?

How many reflections should I be rejecting? How do I treat data that contains an anomalous signal? How do I do this?

How to start scaling from. The Resolution of Diffraction Data. Understanding the Scalepack log file scaleui. Appendix – Installation note.