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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The check boxes below-left control what parameters you want to refine to improve predicted and observed spot positions, and a few things about spot size. How do I fix it? The HKL program always manuak the hko2000 symmetry space group for a particular system during “Bravais Lattice” selection process P2 for Monoclinic, P for Orthorhombic, P3 for hexagonal etc.
What mznual the Profile Fitting Radius and how do I determine what it should be? Check that the data runs listed in the table at top left are all the ones you want to integrate, then press Integrate.
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. Experimenters that perform non-commercial research may freely use the program for data evaluation and processing, while collecting data at the beamline.
The HKL-2000 Manual
The current parameters are shown in the Refinement Information panel at top right. Historically it also paid attention to one of the sigma cutoffs perhaps refinement? Make sure you define a Project and Crystal either via the fields in this tab or via the Project tab. What are reasonable values for the error scale factor and what if I need really high ones?
If you’re screening crystals you’ll just use Project and Collect. How many cycles should I refine for and how do I know how to set this? First we have to display an image and perform a “peak search” operation.
Once the integration is complete, should I update the site? For really problematic indexings I try every 10th frame to get an indexing that I believe to be correct and work from there. When centering your crystal be aware that for best results you need to point a translation sled toward the camera and not toward you. The box needs to be several times the size mznual the spot to get a reliable background estimate. Why would I want to put in any other resolution limits?
This is very useful for changing the last image number for an ongoing data collection. Peaks from a number of images for indexing can be selected by clicking on the “Frame” box of the xdisplayf window using the center mouse button before clicking “OK” for the peak search.
The Integrate Sets Button is red.
For weak auto-indexing results it’s best to refine the auto-indexing result in primitive triclinic first and then re-open this table using the Bravais Lattice button in the Index tab. I’ll discuss strategy below – you kanual have noticed the “Multi” button above-right on the panel and that’s where you define the multi-run data collection strategy. Output plots and Error Scale Factor.
How can I make the diffraction image look “better”? 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 useful for finding homologs or calculating the expected number of sulphurs.
Be aware that the Bravais mankal table is responding only to the location of diffraction spots in the frame and not their intensity. So while chosing space groups be aware that different space group choices within a point group basically have the same scaling statistics.
Using HKL for Data Collection at Princeton University
The spot size can be adjusted using the “Integration Box” window on amnual lower left corner of the above figure. As k,B are expected to be smoothly varying they are often restrained during scaling. This information is retrieved mnual the headers of the images. If you selected 2 or 3 data sets e.
But if you particularly want to fix mosaicity during integration e. Scale and B vs Frame: What should I set at the 3D window? What is this for? It introduces a center of symmetry in the data, so that reflections h,k,l and -h,-k,-l have the same intensity. I’ve not yet tested to see if autoProc can process this data smoothly – you may need to pull.
Strategy You will be using Rigaku’s strategy program rather than HKL3K’s own strategy program since the former is aware of the multi-axis goniostat. What is this for?
You need to press the Connect button to get hkk2000 program to talk to the machine – this establishes connections to the servers in the generator itself.
You only see a significant number of fulls on thicker frames, particularly at higher resolutions. Rigaku Strategy program – present in the previous version, using it is now essential since there’s more than one axis to consider. Most of the options on the project screen are a waste of time for the simple purpose of crystal screening.