Previous: Installation of calibration files, Next: Setting up the data sets

Starting the HKL GUI: an overview.

In the example that we will be describing we have two data sets of ammoniumbitartrate on CD/ROM. One was collected at detector swing=0 degrees, and the files are named 9605_001.kcd up to 9605_090.kcd; the other at detector-swing = 40^o. (theta=20^o) and the files are called 9605t001.kcd up to 9605t090.kcd.

In the second set there is one image which does not contain any reflections. Whereas in the previous version you had to edit a number of command fles to get this set processed, things are now a lot easier an this example will show you.

Moreover, the two sets can now be processed and scaled in one go. The present GUI version however does not yet support kappa offsets. For this you should use the utility nprocess after you have found out the best processing parameters using the denzo GUI.

"cd" to the directory where you have collected your images, and type "kc" there. At startup the Denzo-SMN program will retrieve the settings from the file def.site in the calibration directory. To find out the proper calibration directory, the "kc" program will retrieve the detector number from one of the images in the directory.

The system will come up with the Denzo-SMN window. The window has pull-down menus and cards. The cards will guide you through the measurement in a logical sequence from left to right. The pull-down menus are used for general setup and file handling of the program, and give additional information during the actual data processing.

Menus

On the top you will find the different selections for the program: File, Options, Principal Component, Site configuration, Crystal information and Detector Control.

File

With File you can select to Load or Save so-called "sav" files, which contain the information on an experiment, or you can Quit the program, without saving.

Options

With Options you can select the operator level: Simple or advanced. For an advanced operator the program will present more parameters to change, e.g. the size and shape of the integration box.

Principal component

Principal component will help you to select the content of the crystal (protein, RNA/DNA/Protein, Small molecule or virus) and the proper default values belonging to the application.

Site configuration

Site configuration has the detector, source and goniometer parameter of the equipment used to collect the data.

Crystal information

Crystal information has all the information about the crystal, as far as it is known, like unit cell, orientation, space group and some comment.

Detector control

The selection "Detector control" is not yet active for the KappaCCD.

Help

Help will give a short summary of this file.

Cards