Setting absolute scale with water

This section teaches you how to set up absolute scale using water as a reference. Note that you can use water or glassy carbon (Part 5) for absolute scale calibration in RAW. Glassy carbon is the more accurate approach, if available.

Note: The calibration dataset used for the first parts of this tutorial doesn’t have the requisite data to use for this part. So we will use the data in the calibration_data/extra folder.

A video version of this tutorial is available:

The written version of the tutorial follows.

  1. Load the SAXS.cfg file in the calibration_data/extra folder.

  2. Plot all of the MT2_48_001_000x.tiff files, where x is 0-9, on the main plot.

  3. Average the MT2 files you just loaded. Save the average in the calibration_data folder.


  4. Repeat steps 1 and 2, plotting, averaging and saving, for the water2_49_001_000x.tiff files.

  5. Open the Options window by selecting “Advanced Options” in the Options menu.

  6. Click on the Absolute Scale section in the options list on the left.


  7. Click on the Empty cell “Set” button and select the A_MT2_48_001_0000.dat file.

  8. Click on the Water sample “Set” button and select the A_water2_49_001_0000.dat file.

  9. Set the Water temperature to 4 C.


  10. Click the Calculate button to calculate the Absolute Scaling Constant. You should get a value near 0.00077.

    • Tip: You can also use images to set the absolute scale. This may give worse results, as the signal to noise of the averaged file should be better than for a single image.
    • Note: It is important that you not change your normalization settings once you have set the absolute scaling constant. If you do, you will have to recalculate the absolute scaling constant. Also, make sure absolute scale is turned off before you calculate the scale constant, otherwise you will get a bad scaling constant (see the manual for details).


  11. Check the “Normalize processed data to absolute scale” checkbox. Click “OK” to exit the advanced options window and save the changes.


  12. Save the settings for later use.