HKL tutorial -- How to DENZO



In this tutorial you will process a set of imaging plate images with the HKL suite of programs. This suite consists of the xdisp, denzo, and scalepack programs.

  1. Login to the computer.

  2. Open a shell or command window.

  3. Create a new subdirectory for your work and change to the subdirectory that will be used for your processing by typing:

    mkdir mydir
    cd mydir (Choose your own name for mydir.)

  4. Copy the files required for the HKL tutorial into the current directory by typing:

    hklsetup

    This will copy the following files to your working directory:

    setup.input
    autoindex.input
    refine.input
    integrate.input
    denzo.com
    scale.com

  5. The file setup.input contains some input commands to denzo. Edit the setup.input in another window with a text editor (e.g. jot, emacs, xemacs), so that it contains the information that you know about your detector, goniometer, source, crystal, images, and integration properties.

    jot setup.input &

    Be sure to save your edited file when you are done.

  6. Run the HKL display program xdisp to view your first image to process by typing:

    xdisp raxis4 100 name_of_first_image_file &

    if your images are 100 micron R-AXIS IV images or

    xdisp raxis name_of_first_image_file &

    if your images are 100 micron R-AXIS II images.

    Be sure to change name_of_first_image_file to the name of the image that you want to display. For this tutorial the name of the first image file is ../lyso/lyso11.osc.

  7. Run the HKL denzo progrwn by typing:

    denzo

  8. Now tell denzo about your situation by reading in the setup.input file that you edited:

    @setup.input

    There will be no prompt or other feedback from denzo from this, unless you have mistakes in your setup.input file.

  9. Move your mouse/pointer into the xdisp window. Explore the buttons and commands available. Pick peaks in the image by selecting the Peak Sear button.

  10. After you have picked peaks (Step 9), then you can auto-index the peaks you have found. Do this with denzo by reading in the autoindex.input file into denzo:

    @autoindex.input

    Examine the results of autoindexing. If not satisfied with the space group selection, edit the setup.input file and add the command space group desired_spacegroup_symbol to the [crystal] section of the file, then go back to step 7 (you may skip step 9).

  11. In denzo, refine the autoindexing solution by entering the refinement commands by reading in the refine.input file:

    @refine.input

    You may wish to edit refine.input to implement a specific refinement strategy.

  12. In denzo, change the integration box parameters and crystal mosaicity to match your experiment. View the effects of your changes in the xdisp window. BUT for changes to take effect in the xdisp window, you must enter go in the denzo window. For example,

    box xsize ysize
    spot elliptical x y tilt
    background elliptical x y tilt
    mosaicity mosaicity_value
    go

  13. When you are satisfied with your refinement and integration parameters, copy the refinement results to your setup.input file. To do this, enter the list command in the denzo window. Copy the output to the editor window (cut and paste with the mouse is the most convenient). Manually change the box, spot, background, and mosaicity parameters by editing the file. Save the edited setup.input file.

  14. Exit from denzo by typing stop in the denzo window.

  15. Run the denzo.com shell script to integrate all your images. Enter:

    denzo.com >&! denzo.log &

  16. When the denzo.com script is finished, run scalepack. First edit the scale.com script:

    jot scale.com &

    You will want to change the starting and ending sector. Perhaps you will want to change how post-refinement is done. This will be discussed in the tutorial. When you are done editing be sure to save the modified scale.com file.

  17. Run the scale.com shell script to scale all your reflection files. Enter:

    scale.com >&! scale.log &

  18. Examine the results. You may need to reject reflections and re-run the scale.com shell script.

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    This page was last updated on June 19, 1997.

    J. W. Pflugrath, Molecular Structure Corporation