Fluorescence Scans

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AutoEdge scanning in MxCube

In MAD experiments the wavelengths that maximise the anomalous signals from an incorporated scatterer can be calculated from a fluorescence scan carried out across the absorption edge.
The fluorescence scanning process is fully automated at BM16 and is carried out within MxCube by following the steps below.

1. Click on the Energy scan tab (top right of MxCube GUI).
   
   
2. Select the edge you wish to scan from the periodic table (Most of the commonly used elements are displayed but if the absorption edge you need is not listed ask your LC to add it).
3. Check that the correct pathway has been set in the Directory box. Normally this will be the current directory you have created to collect your data but you can browse to select another directory to write you data into if you prefer.
   
4. Click Start scan to begin the auto Edge scan routine.
   

5. Note: The scan will take several minutes. The energy of the beamline will be changed to that of the selected edge and the diffractometer will be automatically realigned. Then the fluorescence detector will be moved into position. The beam will be automatically attenuated so that the MCA coupled to the fluorescence detector does not become saturated and an energy scan will be carried out and displayed in real time in the MxCube GUI.

6. At the end of the scan Autochooch pipes the calculated optimum energies for the peak and inflection point datasets both to the MxCube GUI and to the PX session. It saves all the relevant Chooch files including a postscript file of the calculated anomalous scattering factors against energy in the directory selected. All fluorecense scans files are saved with the image prefix, the element, the edge and a timestamp.
7. At the end of the scan, all attenuators are removed the fluorescence detector is placed back in the Home position and the safety and fast shutters are closed.

Autochooch utilities

To rerun AutoChooch manually. Find the PX session (usually iconised on the tool bar of bm16mach) and type;

PX>autochoochfordummies

To display the postscript file generated froma plot of the calculated anomalous scattering factors against energy. Type;

PX>autochoochprint

To change the name of a scan, type;

PX>ae_newfile

in the PX window on bm16mach. This will prompt you for a new file name.

Note: only give the prefix! SPEC will use this prefix and the present date to name the file in the directory above.

Some useful tips on running Chooch manually can be found here.

Doing Edge scans outside of MxCube

Fluorescence scans can also be done outside of the MxCube interface by typing the following in the PX session...

PX>energy_scan [Element] [Edge]

eg: energy_scan Se K (Note: give the 1st letter of the element and the edge in caps)

This macro will automatically move the beamline to the appropriate energy and will realign the diffractometer. It will then prompt you for your proposal number and a file containing the scan data will be written to your main data directory with a file name given by the date and the edge scanned.

For a listing of theoretical absorption edges see here.

If you want to check the whole spectrum as you are not sure which elment you have incorporated in your sample click here.