Chapter 1: Starting the Program and Setting the Data Sets
Step 2: Detector and Site info
Choose your detector and site info from the menu.
A site definition contains the X-ray detector and camera information, like the detector name, the goniostat misalignment, direction of rotation, detector orientation, X-ray beam properties, and the expected suffix for data files arising from this site (e.g. *.img, or *.osc, etc.). It also has the default or updated (current) X and Y coordinates of the direct beam position on the detector, a crucial piece of information. This information is stored in /usr/local/hklint or in $HKLDIR as a series of subdirectories, one for each site you might have (Figure 1). Each detector needs an individual site file called def.site. These subdirectories are also where detector calibration data (in the form of files called def.cal and denzo_nonunf) are stored. These files are necessary for processing un-calibrated data. For synchrotron data processing, these files should be obtained from the synchrotron beam-line.
Figure 1. The list of directories with the def.site files
Well, then you have to create a new site definition. You cannot process data if the program does not know what sort of system you were using.
To make a new site, click on the new site button. It then opens a new window with a field to give the new site name. This will create a new subdirectory in /usr/local/hklint with the name you give. It's best to use a descriptive name, like, our_beatup_raxis, or ALS-BL8.2.2-Apr2006-ADSC-Q315 (Figure 2). Now click on the detector type button, and find your detector. Some detector manufacturers have different models and these are listed under each general detector heading. If your detector is not listed at all (unlikely, but theoretically possible), you are out of luck and will have to contact HKL Research (or your beamline coordinator) for the appropriate site file. Once you've selected the correct detector, hit OK. You will now get the main HKL‑2000 window.
The newly created def.site file will contain default values for the X Beam and Y Beam Positions and they are almost always incorrect. You can change these by clicking on Site Configuration, and make the changes here. The un-preferred alternative is to edit the appropriate line in the def.site file in the newly created subdirectory.
Figure 2. The New Site window
Choose the appropriate goniostat from pre-defined list (Figure 2). Presently the following goniostats are available:
single axis – most common
vertical euler – goniostat used with Rigaku Rapid, Saturn and Raxis HTC detectors
nonius kappa – goniostat used by Nonius KappaCCD and Kappa2000 systems
bruker fixed kappa – used with Smart 1000 and Smart 6000 Bruker systems
p4bruk – P4 goniostat used with Smart 6000
aps 19id – minikappa goniostat used on id19 (undulator) beamline at the APS
aps 19bm – minikappa goniostat used on bm19 (bending magnet) beamline at the APS
Note that not all goniostats are pre-defined.
Click on Site Configuration on the top menu bar and this will bring up a window with the site parameters (Figure 3). You can verify that the detector is the right one, and you can specify things like the X Beam and Y Beam Positions and the Wavelength and so on. There are a couple of things to note about this window:
First, you can load in an existing site file by clicking on load site info. This brings up a file navigation window where you can choose a detector site file (def.site).
Second, the wavelength for rotating anode X-ray sources is specified in this window, while the wavelength for synchrotron X-ray wavelengths is specified from the main HKL‑2000 window (and is hopefully, but not guaranteed, to be correctly specified in the image file header – check to make sure!).
Third, clicking on save site info means that you are permanently editing or updating the file called def.site (in /usr/local/hklint/whateverdetector). For this you will need a password, which you may not have as password is provided to the Contact Person. So this is not a typical user option. Also, you must have permission to write to the directory (/usr/local/hklint/whateverdetector, but see the next comment, below).
Fourth, however, you can use your updated site parameters by clicking close button and these will remain in force until you quit the program, after which time they will revert to the original values.
Figure 3. The Site Configuration window
Well, most likely the indexing and integration will fail because file formats will be unreadable, etc. If you are lucky and the detector is correct and the goniostat description is correct you may be able to get somewhere.
The windows describe the six mis-settings angles of a particular goniostat. The choice of single axis goniostat allows for only first two mis-setting angles to be entered:
1) angle around the beam
2) angle describing the non-perpendicularity of angle between beam and omega/spindle axis
The 19id, 19bm vertical euler and kappa ccd goniostats, require all six mis-settings angles to be defined. The four remaining angles are:
3) Omega zero
4) Deviation between nominal and actual kappa (chi) – omega angle
5) Kappa zero
6) Deviation between nominal and actual kappa (chi) – phi angle
The change of spindle axis direction requires the change of first mis-setting angle by 180 degrees. This is equivalent to old style command to HKL film rotation 180.
How do I start the HKL-2000 program?
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