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 you want to do some form of postrefinement even amnual it’s not immediately obvious which of the options is most appropriate and in anything except pathological cases there is little difference. When HKL starts it defaults to a generic project name – it doesn’t save your old project info so you should remember to save it manually before quitting and load it after starting.
Setting up Data Files. Should I click Show all Files? The data directory contains raw diffraction images recorded to the maximum resolution of 2. How do I stop and start over? This will include that command on the macro area below. What you’ve done is scale all the data runs lumped together, minimizing the discrepancies between symmetry-related reflections.
Should I click Show All Manuxl Due to the scattering of an atom we can see how the reflection intensity decreases in higher resolutions. What are reasonable values for the error scale factor and what if I need really high ones? How do I get back to P1? Can I add some peaks that I think the autoindex should use? This will launch the HKL window and it will also show information about the other programs running on the machine in a red box as shown below.
What is the Error Scale Factor and which way should I adjust it? The buttons on the left are the important ones.
HKLR effectively controls the goniostat and detector, indexes data, calculates strategy and processes the data. How do I change it? Why would I want to do this?
What is a site definition? How to do this with Scalepack?
If you have two screw axes, then your space group is P, with the screw axes along a and b. What is an acceptable range for Chi2? Output plots hkl20000 Error Scale Factor. For integration you basically only need to produce a good correlation between predicted and observed diffraction maxima – some changes in Bravais lattice can be accommodated in scaling even if you’ve integrated it as the lowest symmetry primitive triclinic.
Data Processing In a perfect world a data strategy program would guarantee that your data collection will result in complete, redundant data without you having to check. Please note that the indexing procedure always takes the “beam position” values from the “Site Configuration” file. Red selections circles should appear. The “Macros window” below shows the incorporation of “no merge original index” flag during scaling. It’ll take a few seconds to do this and then the GUI will parse the Scalepack log file and populate the graphs in the upper mnual of the scale tab with a summary of the Scalepack log file.
Yellow and green reflection centroids are partials and fulls, respectively. I’ll discuss strategy below – you might have noticed the “Multi” button above-right on the panel and that’s where you define the multi-run data collection manjal. To remove irrelevant data runs, press Select in the blue box and then Remove Set in the Set Controls panel.
Selections are not possible on a zoomed window. Scalepack then reads all these. Appendix – Installation notes. Please note that the current version of HKL doesn’t work well if you change the hkl200 number after indexing the frames.
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The initial quality of that software was relatively poor with manua, functional bugs including one or two dangerous ones. 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.
Inherently a number of semi-empirical parameters are refined to minimize the intensity differences between observed reflections that should have the same intensities based on symmetry. The “Integration Information” panel at lower right will show you positional chi 2unit cell parameters etc during integration.
Can you explain it?