Loading configuration files and images, creating subtracted scattering profiles, saving profiles
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. _s1p1:

#.  Open RAW. The install instructions contain information on installing and running RAW.

#.  In the files tab, click on the folder button and navigate to the
    **Tutorial_Data/standards_data** folder. Click the open button to show that
    folder in the RAW file browser.

    |file_ctrl_1_png|

#.  At the bottom of the File tab in the Control Panel, use the dropdown menu to
    set the file type filter to “CFG files (\*.cfg)”.

    |file_ctrl_3_png|

#.  Double click on the **SAXS.cfg** file to load the SAXS configuration.
    This loads the beamline configuration into the program.

    *   *Note:* Any time you are going to process images, you need to load the appropriate configuration!

#.  Change the file type filter to “TIFF files (\*.tiff)”.

#.  At the CHESS G1 station, typically ~10 images are collected from a given sample. To load in the 10 images
    for the glucose isomerase (GI) sample, start by selecting the files
    **GI2_A9_19_001_xxxx.tiff**, where **xxxx** will range from **0000** to **0009**\ .
    These files are measured scattering from 0.47 mg/ml GI.

    *   *Tip:* you can hold down the ctrl key (apple key on macs) while clicking to select multiple files
        individually. You can also click on a file, and then shift click on another file to select those
        files and everything between them.

    *   *Warning:* Don’t load the files with **PIL3** in their name. Those are the wide-angle
        scattering (WAXS) data, which we will process separately later.

#.  Click the plot button to integrate all of the images and plot the integrated scattering profiles on the Main Plot.

    *   *Note:* Typically, once the images are integrated we work only with the scattering profiles.
        However, it is useful to keep the images around in case you want to reprocess the data.

    |file_ctrl_2_png|

#.  Plot the **GIbuf2** scattering profiles from the images. These are measured
    scattering from the matching buffer, without any protein, for the GI sample.

#.  Click on the Manipulation tab. This is where you can see what scattering
    profiles are loaded into RAW, and manipulate/analyze them.

    *   *Checkpoint:* If you’ve successfully loaded the images given, you should see twenty
        scattering profiles in the manipulation list, with names like **GI2_A9_19_001_0000.tiff**
        or **GIbuf2_A9_18_001_0000.tif**.

    |manip_items_1_png|

#.  Click on a filename to select the scattering profile. The background should turn gray, indicating it is selected.

    |manip_items_2_png|

#.  Select all of the GI scattering profiles

    *   *Tip:* Again, the ctrl(/apple) key or the shift key can be used
        to select multiple scattering profiles.

    *   *Warning:* Select only the GI profiles, not the GI buffer profiles.

    |manip_items_3_png|

#.  Use the average button to average all of the scattering profiles collected into a single curve.

    *   *Checkpoint:* The averaged scattering profile should appear at the bottom of
        the manipulation list. You may have to scroll down to see it. The filename
        will be in green, and will start with **A_**, indicating it is an average scattering profile.

#.  Average all of the GI buffer scattering profiles.

#.  In order to see the averaged scattering profiles, you will need to hide the
    individual profiles from the plot. Clicking on the check box to the left of
    the filename will show/hide a scattering profile. When the box is checked,
    the profile is shown on the plot, when it is unchecked, the profile is hidden.
    Hide all of the profiles except the two averaged curves.

    *   *Tip:* The eye and eye with the x through it at the top of the manipulation panel
        can be used to show/hide sets of loaded profiles at once. If no profiles are selected,
        these buttons show/hide all loaded profiles. If some profiles are selected, these buttons
        show/hide just the selected profiles. Try selecting all but the averaged files and using
        the show/hide all buttons.

    |manip_items_4_png|

#.  Next you need to subtract the buffer scattering profile from the measured
    protein scattering (which is really the scattering of the protein plus the
    scattering of the buffer). Star the averaged buffer file, and select the
    averaged protein file, then click the subtract button.

    |manip_items_5_png|

    *   *Checkpoint:* The subtracted scattering profile should be shown in the lower plot. A new manipulation
        item should be shown in the manipulation menu, with the name in red and a **S_** prefix
        indicating it is a subtracted file.

    |manip_items_6_png|

#.  You don’t need the individual image scattering profiles any more. Select all of those
    (but not your averaged or subtracted profiles!) and click remove.

    *   *Note:* This only removes the scattering profiles from RAW. The images on your
        hard drive are unaffected.

#.  Load in the **lys2** and **lysbuf2** files, average, and subtract to create a subtracted lysozyme
    scattering profile. The concentration of this sample was 4.27 mg/ml. Remove all of the profiles
    that are not averaged or subtracted profiles.

    *   *Tip:* In order to tell which curve is which in a plot, click on the target icon in
        the manipulation list. This should bold that curve in the plot. Click the target icon
        again to return the curve to normal.

    |manip_items_7_png|

#.  We’re done with the averaged profiles. Select all of the averaged profiles and click the “Save”
    button to save them in the **standards_data** folder. Note that in the filename in the manipulation
    list, the * at the front goes away. This indicates there are no unsaved changes to those scattering
    profiles. You can now remove them.

    *   *Note:* This saves them with a **.dat** extension. This is the standard format for SAXS
        scattering profiles, and is also human readable.

    |manip_items_8_png|

#.  Right click on the subtracted plot, move the cursor over ‘Axes’ and select the Log-Log option.
    Well-behaved globular proteins will intersect the intensity axis roughly perpendicularly.

    *   *Note:* It is best practice to display SAXS data, particularly in publications, on either
        a semi-log (Log-Lin, default option in RAW) or double-log plot (depending on the features
        of interest).

    |log_log_plot_png|


.. |file_ctrl_1_png| image:: images/file_ctrl_1.png

.. |file_ctrl_2_png| image:: images/file_ctrl_2.png

.. |file_ctrl_3_png| image:: images/file_ctrl_3.png

.. |manip_items_1_png| image:: images/manip_items_1.png

.. |manip_items_2_png| image:: images/manip_items_2.png

.. |manip_items_3_png| image:: images/manip_items_3.png

.. |manip_items_4_png| image:: images/manip_items_4.png

.. |manip_items_5_png| image:: images/manip_items_5.png

.. |manip_items_6_png| image:: images/manip_items_6.png

.. |manip_items_7_png| image:: images/manip_items_7.png

.. |manip_items_8_png| image:: images/manip_items_8.png

.. |log_log_plot_png| image:: images/log_log_plot.png