The Data Collection GUI is started simply by double-clicking the MXDC icon on the desktop.

This will start the program. The GUI is organized into tabs, with each tab allowing access to different functions of the software.

The functionality of each tab is described is the respective sections below.

 

This tab is used for setting parameters such as Energy, Attenuation, Beam size, Detector Distance, Detector 2Ө (to be implemented), Beamstop position, and Goniometer Omega. Below is a screenshot of the Beamline Setup tab.

The functionality of each button is described below.

Prepare for Mounting:

The Prepare for Mounting button is used to prepare the hutch for mounting crystals. This button will move the detector and beamstop out of the way to make space to mount your crystal. After mounting the crystal, you will probably need to align within the Sample Camera pane described below.

Sample Camera and Sample Alignment

The Sample Camera pane shows a live view of the crystal and has a few simple buttons to help you align the your crystal.

Zoom Level:

If the crystal is not visible, you may need to decrease the zoom level using the zoom level buttons.

Move Sample:

To get the crystal in the field of view or for manual centering, you may used the move sample buttons.

Rotate Sample by:

The sample needs to be rotated as part of the alignment process to ensure the axis of rotation of the crystal intersects the beam. The crystal is aligned by centering the crystal as described below.

Centering:

Manual point and click centering is activated by selecting the 'Click' button, within the Sample Camera tab in the MX Data Collection GUI.  The crystal is aligned as follows:

1. Select a low Zoom Level to find the sample.
2. Activate 'Click' Centering and Click on the sample to center it.
3. Rotate Sample By +90 (or -90) degrees.
4. Click on the sample once again to center.
5. Select a high Zoom Level.
6. Repeat steps 3 to 4 to align the crystal accurately.

After aligning the crystal you should check the beamline parameters and adjust them if necessary.

Beamline Parameters

The beamline parameters shown above (Energy, Attenuation, Beam Width, Beam Height, Goniometer Omega, Beamstop position, Detector Distance, and Detector 2Ө (to be implemented), can be adjusted by entering the desired value in the editable box on the left (the box on the right shows the current value). After entering the value, you must either hit ENTER or click the right-arrow to apply the value. While the parameter changes, you will see its value updated in the current value box, and the right-arrow will turn into a stop button that you may use to cancel a parameter change. The curved left-arrow may be used to revert to a previous value.

Energy (keV):

The Energy box is used to select the energy of photons that reach the sample in the endstation. This is achieved by moving the monochromator to the appropriate Bragg angle. This box is useful for setting the energy that you wish to take a snapshot of the crystal at.

Attenuation (%):

The Attenuation box is used to control the percentage of photon that are transmitted to the sample in the endstation, and hence the intensity of diffraction spots on the detector. If the diffraction spots are too intense, you may either increase the attenuation or decrease the exposure time. The attenuator has four thin foils of aluminium that are set according to the desired attenuation. The current value of the attenuation is calculated based (with beam energy taken into account) on the actual foils used.

Beam width (mm):

The Beam width box allows the user to control the width of the JJ slit collimators that trim the beam in the horizontal direction.

Beam height (mm):

The Beam width box allows the user to control the width of the JJ slit collimators that trim the beam in the horizontal direction.

Omega (deg):

The Omega (deg) box allows the user to control the rotation angle of the sample goniometer.

Beam-stop (mm):

The Beam-stop (mm) box allows the user to control the distance of the beamstop from the sample (it can approach to within about 5mm and extend out to about 45mm). The further the beamstop is from the sample, the larger its shadow will be on the detector.

Detector Distance (mm):

The Detector Distance (mm) box allows the user to control the distance of the detector from the sample. The detector distance may also be set from within the Data Collection tab, but the value entered hear will become the default value.

Detector TwoTheta:

This feature is not available directly from the GUI at the moment, but the detector can be put into the appropriate position

 

The data collection tab is used to setup crystal screening parameters and run parameters for collecting single or multi-wavelength datasets. Below is a screenshot of the Data Collection tab.

Run Tabs:

The data collection GUI is capable of handling multiple runs with different parameters (e.g. detector distance, exposure time). The user is free to add and delete tabs except the Run 0 tab, which is for screening crystals. Run tabs are added using the Plus button and deleted using the Delete button.

The Run 0 tab includes a resolution predictor to assist the user in determining a suitable distance for the detector. When the Run 0 tab is selected, clicking 'Collect' will just take a snapshot of your crystal (frames in other runs will not be collected). If you wish to take another snapshot, without erasing the previous snapshot, you may do so by incrementing the number in the Start Frame box.

Run Parameters:

Enter parameters into the data collection application such as the directory you wish to store your data in, prefix for the image file names, distance of detector, omega delta, start frame and end frame. The following is a list of parameters and definitions:

• Prefix: The prefix is the first part of the name in the image files generated.
• Directory: This is the file directory where your images will be stored.
• Distance: The distance between the sample and the detector.
• Delta: Degree of rotation during exposure (commonly 1 or 0.5 deg, depending on spot overlapping).
• Time:  Length of exposure time in seconds.
• Start: The frame number and omega value assigned to the first image.
• End: The frame number and omega value assigned to the final image.
• Inverse beam: Rotates the crystal by 180 deg to collect the Friedel pairs for the input omega range. If wedges are used, the inverse beam is collected before changing the energy.
• Wedge: The omega rotation range that is collected successively at each energy.
• Energy: As you enter every new energy, an empty box appears for further energy entries.

Save Button:

The Save button takes all the run parameters that have been entered in each tab and sets up a queue for frames that will be collected.

Undo Button:

The Undo button undoes the most recent Save.

Delete Button:

The Delete button deletes the current run tab.

Queued Data Collection Frames:

The frames that are queued for data collection are displayed as a scrollable list. Uncollected frames have an unchecked box beside them, whereas collected frames will have a checked box beside them. It is possible to pause the data collection process once it has been started and resume at a frame of your choice. This is done by selecting the desired frame and clicking resume.

Collect Button:

After the run parameters have been defined and saved into the queue, data collection may be started by clicking the Collect button.

 

The fluorescence scan tab is used for MAD and excitation scans. Below is a screenshot of the Fluorescence Scan tab. The MAD scans (or energy scan) is used to select the appropriate wavelengths for anomalous dispersion experiments (optimized SAD and MAD). The excitation scan is used to identify and or verify the presence of anomalous scatterers in the sample.

For a MAD scan you must first select the element from the Periodic Table tab by clicking on a particular edge (K, L1, L2, L3) and you may continue and press the Scan button.

The scan mode is selected by using the radio buttons user "Scan Mode:" The results are placed in the chosen directory (to the right of "Directory") and the file name is derived from the string entered as the "Prefix."