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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What if no lattice other than primitive triclinic comes up green?
What is the error model and should I adjust it? What is this for? In this exercise you will learn how to process raw diffraction images and how to go through data reduction to a set of intensities or structure factor modules. As such, unless you really know what your space group majual for this HEWL crystal it’s P4 3 2 1 2 then the strategy is really an educated guess that must be verified during scaling.
The current limits on goniostat angles are: Comparison with HKL You might have encountered HKL at the synchrotron – in some cases it’s used as the default method to process data and can be useful because it shows the predictions vs observed reflections in real time. How do I stop and start over? 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.
Running HKL at SSRL
How long is this supposed to take? This is very useful for changing the last image number for an ongoing data collection. Generally speaking be ultra-cautious about driving the goniostat into positions manually – drive them perhaps half-way and visually check for potential collisions. Scalepack is the program that does the scaling. Then middle-mouse click on the Frame button at top right in XDISP to load the next image, which will also peak search and the peaks added to the list.
The per-frame correction factors model things 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 fall-off in scattering with respect to resolution.
If you’ve used HKL then the general layout is familiar. Denzo presents this table of possible indexings in the “Bravais Lattice Table”.
The HKL-2000 Manual
Waiting for image frames. Scroll down in the graphical data tables to see some statistics with resolution or by frame number. In any event, all scaling methods involve exploiting the redundancy in your data as a method for estimating the quality of the scaling result is going to improve as the redundancy of your data improves.
In the display window lower right window you can see how the different parameters change as the crystal rotates from image to image during the exposure large fluctuations may indicate experimental problems. If you need a copy of the default file, for this or any other of the detectors used at SSRL, please contact Msnual Mathews. Set the “Raw Data Dir” to the directory where the images are located.
Parts of the original rant may slip through the edit, or there may be new reasons to rant. You can create new projects, save existing ones, load old ones. Do I have to have a. What is the error model and should I adjust it?
Using HKL for Data Collection at Princeton University
How much disk space am I going to need for this? How do I do this?
The buttons on the left are the important ones. On this image – collected with 0. Similarly select “Small Slippage Imperfect Goniostat” to activate postrefinement. What is an acceptable range for Chi2? At left here is the manuap factor and B-factor by frame which you expect to move around smoothly but perhaps jump a little at the boundaries between kanual runs. Check that the data runs listed in the table at top left are all the ones you want to integrate, then press Integrate.
Where do they go?