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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Usually the HKL program is started either from the data collection directory or from a “process” sub directory under the data collection directory. In the Zoom window you should be able to see the individual pixels of the detector, each with its own degree of blackness, proportional to the number of X-ray quanta accumulated during the exposure.
The Collect is by far the most important tab. Do I have to have a. How many cycles should I refine for and how do I know how to set this? How do I do this? What is a site definition? 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. To refine the initial indexing result e.
What is the error model and should I adjust it? Understanding the Scalepack log file scale. How do I do this? In addition, the diffraction power may decay over time due to radiation damage, or due to poor cryo-protection as ice rings develop. It looks like I can put in more frames than I actually have.
The computer is always left running, usually logged in, usually running the Linux side of the dual-boot setup.
The HKL system also has tools for validating the results by self-consistency checks. It’s not a perfect world.
The HKL-2000 Manual
Experimenters that perform non-commercial research may freely use the program for data evaluation and processing, while collecting data at the beamline. Something less than 1. Make sure the data runs you want to merge are included in the “Pending Sets” list. It also provides more accurate estimates of the Lorentz correction which can be large for low resolution reflects that lie near the rotation axis.
What is the 3D Window? Manuaal if I want to process some of the hk2l000 in this set separately?
Using HKL for Data Collection at Princeton University
Here you can see some disjoint behavior for the last few runs 20 frames each, so 5 degrees and you might hjl2000 tempted to omit them from scaling – at the bottom there’s a button for Exclude Frames to allow you to omit some especially troublesome frames, but in this case you’d hkl200 go back to the Data tab and deselect the Scale checkbox for any runs you want to delete in their entireity.
What should I set at the 3D window? What is a site definition?
When you scroll the scalepack output window from top to bottom, you will have the following graphs: The primary space groups are the first space groups in each Bravais lattice type in the table below. Detector and site info.
Running HKL at SSRL
These graphs can be viewed by moving the sliding bar hkl2000 the right side of this window. This will bring up a small “Beam Position” window with detailed informations on how to select the beam position by clicking on a displayed image.
To reload an existing project, use the Load button within the Project tab and locate the relevant. Rigaku Strategy program – present in the previous version, using it is now essential since there’s more than one axis manuxl consider. 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.
The fundamental stages of data analysis are: The refined parameters are visible in the upper right portion of the screen.
The completeness is plotted versus intensity of the reflections. To determine your space group, follow these steps: Starting the Program and Setting the Data Sets. The HKL program will always select the lowest symmetry space group for a particular system during “Bravais Lattice” selection process P2 for monoclinic, P for orthorhombic, P3 for hexagonal system, etc. Indexing of the data to figure out the Laue class, Bravais lattice and cell dimensions.
What are the limitations for hkp2000 Window usage? How many peaks do I want to use? Phenix are likely to be added in the near future. In the xdisp window all reflections should be present in the yellow prediction circles.
I don’t necessarily agree with all of those decisions either, but it gets me pretty close to the desired end-point without me having to click any buttons. Data Collection loads the sort of parameters you’d use if you actually want to collect an entire dataset.