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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Is the number of selected peaks sufficient for indexing? Profile Fitting Radius sometimes gkl2000 to be increased for particularly weak or anisotropic data or Denzo will refuse to integrate weak data with insufficent nearby strong spots to estimate the profile from.

If you turn on absorption correction it will additionally refine an empirical absorption manuaal parameterized as spherical harmonics. Can I click more than one set of data? Normally the correct number is found automatically, but you can use this to exclude ranges of frames at the start or end of nkl2000 set from processing. 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 hkl000 for finding homologs or calculating the expected number of sulphurs.

Mosaicity estimates are sometimes problematic for crystals with streaky spots, and if the refined mosaicity climbs too high it will likely cause problems with spot overlaps spots whose centroids are too close to each other on the frame.

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Running HKL at SSRL

The Distance that came up in the Experiment Geometry window is wrong. Can I index on another frame?

Click Rigaku Strategy to launch the program. The “Set Beam Position” box is active only when an image is displayed with the “Display” option. Why do the bars in the mosaicity histogram get thicker or thinner? Note that you cannot do any better than this i.

The primary space groups are the first space groups in each Bravais lattice type in the table below. On the lines above primitive triclinic, Denzo permutes and potentially distorts that unit cell to obey the symmetry-mandated requirements for each subsequent Bravais lattice, with highest symmetry toward the top.

The HKL-2000 Manual

Waiting for image frames. Where do they go? How do I do this? How do I verify that the site information is correct? From starting guide and installation process to the step-by-step data processing procedure this book will be manuql valuable resource. The X-Axis value indicate the starting angle. In a new hml2000 window hkl2000 to the end of the log file and locate the “Summary of reflection intensities and R-factors by shells” table. A general view of the “Scaling window” before running scaling program is shown below.

To remove irrelevant data runs, press Select in the blue box and then Remove Set in the Set Controls panel. When you scroll the scalepack output window from top to bottom, you will have the following graphs: What are the three Scalepack output Files?


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.

It also initializes the detector and all axes on the goniostat when it does so – this takes a while since manusl goniostat isn’t all that fast.

Other results, such as indexing of the diffraction pattern, are in most cases only intermediate steps to achieve the above goals. 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 Mamual, Inc.

Can I add some peaks that I think the autoindex should use? How do I treat data that contains an anomalous signal?

What is the Reference Zone? What are all those the Refinement Information values for, and what do they mean? That’s the icon right next to the System menu. Low resolution vs completeness: Can I click more than one set of majual