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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Select the Scale tab. Controlling the Machine The control computer is dual boot – one side of it is a Centos Linux operating system running HKLR to control the machine and the flip side is a Windows 7 operating system running CrysAlis Pro.
The per-frame correction factors model ukl2000 that vary primarily with image number, of which primary absorption and scattering effects due to the variation of the volume of the crystal in the beam are the main one, and a B-factor term that potentially models the impact of radiation damage on the crystal manial in scattering with respect to resolution. What if I want to process some of the frames in this set separately?
Once you’ve got enough data spots selected – and sometimes Manuaal select an abundance of spots on the frame and let Denzo sort out the wheat from the chaff – press the INDEX button in the Index tab. Check again the correspondence between predicted and observed spot centroids. The completeness hlk2000 plotted versus intensity of the reflections. I generally recommend against doing this if you’re actually collecting data since it makes more sense to cluster related datasets into one project.
No part of this document shall be hkl200, stored in a retrieval system, or transmitted by any means, electronic, mechanical, photocopying, recording, or otherwise, without written permission from HKL Research, Inc. Scalepack then reads all these. 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.
Running HKL at SSRL
Ykl2000, back to the Collect sub-tab within Collect. What are reasonable values for the error scale factor and what if I need really high ones? The Distance that came up in the Experiment Geometry window is wrong.
Parameter refinement may quite easily fall into false local minima during minimization.
Table of Contents
What is the Reference Zone? What are the three Scalepack output Files? What is the Reference Zone? XdisplayF for visualization of the diffraction pattern Denzo for data reduction and integration Scalepack for merging and scaling of the intensities obtained by Denzo or other programs. I think the direct Beam Position is wrong. If you want to drive to a specific goniostat value, this is where you’d enter it.
The HKL-2000 Manual
Can I click more than one set of data? Clicking on the “Summary” tab shows a short summary of these parameters. There are some behind-the-scenes analytical corrections for Lorentz and polarization factors, air absorption etc but then Scalepack refines a per-frame scale factor k and a per-frame B-factor B as a primary method of reducing systematic differences in the data – i.
Macromolecular Crystallography, part A, p. If you have two screw axes, then your space group is P, with the screw axes along a and b. The hkl2000 one to pay attention to is primitive triclinic all the way at the bottom – this mamual the inherent spot arrangement on the frame and the largest value here corresponds to your smallest inter-spot spacing.
Once you’ve changed the values the blue button at left marked Collect Sets will be enabled and you can collect the images. If this is not the first time you’ve integrated the data you’ll be prompted if you want to overwrite the “.
It looks like I can put in more frames than I actually have. What if the Peak Search picks lots of peaks in the ice ring, or picks peaks from a second lattice?
Similarly select “Small Slippage Imperfect Hkl20000 to activate postrefinement. This way, the peaks will be accumulated off multiple frames – and mnual also appears to improve the mosaicity estimate during initial auto-indexing.
Clicking on each of these parameters at the bottom portion of the graph displays their respective graphs. You can also adjust the error scales in resolution shells via the Adjust Error Model button. Data Collection are the sort of parameters you’d use if you actually want to collect an entire dataset. The Resolution of Diffraction Data.
H,l2000 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. What should I be looking for in the charts that show up after scaling? What you’ve done is scale all the data runs lumped together, minimizing the discrepancies between symmetry-related reflections.
The data directory contains raw diffraction images recorded to the maximum resolution of 2. Is that hol2000 correct resolution in the green box. Indexing and Generating a Strategy You can process your data while it is being collected – recommended – or you can process it later using nkl2000 HKLR program icon this version doesn’t control the hardware. How to launch the HKL package?
Also, the X-ray beam intensity fluctuates with time. Most of the options on the project screen are a waste of time for the simple purpose of crystal screening. What is the 3D Window?