Next: Starting the HKL GUI: an overview

Nonius: HKL software: installing calibration files

To be able to run this version of Denzo, however, some changes need to be made in the location and content of the calibration files for your detector.

1. Logon to the computer as superuser.
2. Create a subdirectory in /usr/local/hklint with as name the number of your detector, e.g. 9605.
3. In this directory put your two calibration files: def.cal and sensi9605.kcd.
4. For the August 1998 version of the HKL software, now edit the file def.cal using your favorite editor.
   • Make the sensitivity file point to the right directory, e.g.:

         sensitivity file '/usr/local/hklint/9605/sensi9605.kcd'
         

   • Make sure there is a line:

         y scale 1.
         

     If it is not there already, please add it.
5. For the July 2000 version of the HKL software, now edit the file def.cal using your favorite editor.
   • Remove the 'sensitivity file' line
   • Remove the 'y scale 1' statement
6. Create the site information

   This is a one-off operation in which you will have to type in the site information of your system. These are the detector parameters which were previously stored in the file initial.set.

   Go to a directory where you have a set of images of the test crystal, which have been collected in YOUR laboratory and which have been processed, i.e. you have the .kcd files and the .x files. Let's suppose there are files called s01f001.kcd and s01f001.x. Now, still as superuser, start the GUI by typing :

   /usr/local/bin/HKL2000
   

   If this results in a complaint about a Tix library, please make sure that the "/usr/local/bin" directory is in your PATH, and then try again.

   A small window will pop up, asking the name of the directory containing your calibration files.

   

   Choose the right directory, in this example 9605. If the site file is missing, the following window will pop up:

   

   Click OK to continue. The following window will ask for the detector type, which in the KappaCCD case is CCD --> CCD nonius binned. Tick the box of this detector type and press OK.

   

   Now the GUI will pop up.

   A new file /usr/local/hklint/def.site has now been created. This contains the default detector parameters, which should be changed to the parameters of your detector. To see the correct parameters of YOUR detector, look at the tail of one the x-files, by doing e.g.

     tail s01f001.x
   

   On the screen you will now see something like:

   Cassette rotx -.27 roty -0.6  rotz .00	These are the Detector Rotation values
   x-beam  29.367 y-beam  28.325	These are two of the Detector Translation values
   crossfire  x .516 y .712  xy  -.010	These are the X-ray beam crossfire values

   Now in the GUI, click on the top of the window: Site configuration. The following window will pop-up:

   

   Now fill in the respective fields of the input window, such that the values correspond to those in the tail of the x-file.

   For a graphite monochromated KappaCCD on a sealed tube, the value for polarization should be -0.0227, for a graphite monochromated KappaCCD on a rotating anode tube, the value for polarization should be +0.0227. After having done this, the window should look like this:

   

   Click the button Save site info to store the corrected values. A small window appears asking for a password.

   

   The password to use is hklint. This is only there to prevent you from doing things you shouldn't do by accident. Fill in the password and click OK. Now everything is ready to process and scale data using the new GUI.

   Exit the program (File, quit).