MAD Data collection on 14.2

MAD Data Collection on 14.2

This page is intended to provide a guide when performing fluorescence scans to determine your optimum peak and inflection point wavelengths for selenium-methionine MAD experiments. Almost always there will be a member of the station staff to assist you during the scan. However, if you have been shown the fluorescence set-up before and feel confident, you may want to perform the scans yourself and this page can be referred to for assistance.

Accessible Absorption Edges on 14.2

	Absorption Edge	Wavelength (Å)	Energy (keV)	Monochromator Scan Range (mdeg)
	Selenium (Se) K	0.97975	12.656	8940 - 9040
	Mercury (Hg) LIII	1.00944	12.284	9210 - 9310
	Rhenium (Re) LI	0.99009	12.524	9030 - 9130
	Tungsten (W) LI	1.02497	12.098	9350 - 9450
	Iridium (Ir) LII	0.96700*	12.823	8820 - 8920
	Osmium (Os) LI LII	0.95574* 1.00129	12.974 12.384	8715 - 8815 9130 - 9230
	Thallium (Tl) LIII	0.97968	12.657	8940 - 9040
	Lead (Pb) LIII	0.95112*	13.037	8670 - 8770
*The limit on the wavelength range means that although these edges are accessible it is not possible to collect a high-energy remote wavelength data set.

Step 1
Screen your crystals for the one that gives the best quality diffraction data.
Step 2
To avoid saturating the fluurescence detector, use PXGEN++ to close the front collimator gaps so the back ion chamber reads about 0.3.
Step 3

Use the Fluorescence button on the OEMove page to open the FluorescenceHeight window.
Drive the fluorescence detectors to their top limit.

Step 4

Select a wavelength of 0.9795 Å.
Go into the hutch and check the steel pointer, on the end of the two theta arm, is above the mark on the blue masking tape (the tape stuck to the floor).
If it is not above the mark:
      1. Move the wavelength again until 
         the pointer is aligned with the 
         mark on the blue tape.
      2. Change 'Mode' to 'Set' and use 
         'Set Position' to set the 
         wavelength to 0.9795 Ang.
      3. Use 'Dismiss' to close the 
         interface.
      

Step 5

Check the fluorescence detector control rack and high voltage power supply are switched on. These are both located inside the hutch, on the left as you enter it.

Step 6
Interlock the hutch and use PXGEN++ to open the shutter, exposing the crystal to X-rays.

Step 7

In the electronics cabin close to the station,
locate the computer '142FD1'

Start the 'PX MCA control' GUI (shown right) by double-clicking the 'PXMCA.exe' shortcut. Select the appropriate element then tick the 'MCA in coincidence' tick-box. A second program called 'PXPC142 MCB1' will then start up.

In this program, select 'Start' within the 'Aquire' menu, to collect the fluorescence signal. Check the peak starts to grow at the correct energy. With the 'Aquire' menu You can stop, clear and restart at any time.

Step 8

Click on the Exafs page of pxgen++.

Select the edge to scan in the table

The scan range is set when the element is chosen, but you can extend it if required. If you choose an element other than selenium, you must ensure the lead plates at the end of the beamline do not block the beam.
Click Start Scan to collect the exafs data.

The monochromator will move to the start of the scan range. At this point you will notice the ion chamber reading go to zero for a second, and then come back again. This is because the 2-theta arm, which carries the whole optical bench, moves slightly more slowly than the monochromator but will catch up.
The software will plot out your fluorescence scan as a graph of fluorescence (y-axis) against monochromator angle (X-axis). The program scales the graph as it proceeds, so what appears to be large fluctuations early in the scan will hopefully prove to be flat background by the end. The scan should look something like this:

Close the shutter when the scan is finished.
Fluorescence Scan Troubleshooting
Some common problems encountered when performing fluorescence scans, and the solutions.

Problems Solutions
The scan is a flat line at zero There is no beam on your crystal or shutter closed or port closed or beam lost or beam misaligned or power supply off or lead plates cutting beam off.
The scan appears to be all noise Ask the user support scientist to check the energy discriminators. Is there any Se in your crystal? Widen the scan range.
The scan is inverted: peak at lower energy The fluorescence detector is overloaded. Reduce the counting time to 0.5 seconds or reduce the beam size or slide the detectors further away from the crystal.
The background level either side of the peak is similar The fluorescence detector is overloaded. Reduce the counting time to 0.5 seconds or reduce the beam size or slide the detectors away from the crystal.
There is a discernible edge but it is noisy The detector is not receiving enough counts. Increase the counting time to 2 seconds or check ion chamber reading is maximised or move the detectors towards the crystal.
There is an edge but it is towards one end of the scan range Ask the user support scientist to check the monochromator calibration or change the scan range.

Step 9
Determine the optimum peak and inflection point wavelengths for your MAD experiment. To do this you can run Gwyndaff Evans' programme Chooch , by typing:

runchooch element filename
(e.g. runchooch se scan.dat)
This will plot your edge scan as a function of X-ray energy.

Type 0 to fit the below-edge background and 0 again to fit the above-edge background. Next, double-click on the image with the left-hand mouse button to produce a smoothed fit to the curve and the anomalous and dispersive peaks.

Click C to continue and the program will display the anomalous and dispersive contributions as shown below. The energies for the peak and inflection point are displayed at the top of the window. You can also pick energies by moving the cursor with the mouse and clicking with the left-hand mouse button.

Once you have determined your peak and inflection point energies (in eV) you will need to convert them into wavelengths (Å). To do this use the tools window that comes up when you load the 14.2 manual front page . Select the "Wavelength/Energy Converter", enter each energy value in eV and click "Calculate". Round your calculated values for the peak and inflection wavelengths to five decimal places.

Step 10
Set the wavelength for data collection.

Always reoptimise the ion chamber signal at the new wavelength, to avoid phi-height problembs.
The limits for the wavelength are 0.95 Å and 1.00 Å for high and low energy remotes respectively. If you are collecting a low energy remote (~1.00 Å) make sure you remove the metal plate in the hutch floor, otherwise the 2-theta arm will not be free to move. When changing the wavelength to one of the remotes you will again notice the ion chamber reading drop to zero for the reasons described above. As this is a relatively large wavelength change it does take about five minutes for the reading to return. It is vital that you do not abort the mono movement during this time.
Collect a highly complete and redundant peak wavelength dataset first (with inverse beam). If you get no other data from your crystal this could be enough to solve the structure. Then collect at the inflection point and finally the remote(s). If you have time and your crystal has not suffered too much radiation damage it may be a good idea to collect a further two datasets approximately 2 eV either side of the inflection point.
At the end of your experiment please remember to set the wavelength back to 0.9795 Å for the next users.

Running SOLVE for Anomalous Data

	Use the Fluorescence button on the OEMove page to open the FluorescenceHeight window.
Drive the fluorescence detectors to their top limit.

In the electronics cabin close to the station, locate the computer '142FD1'
Start the 'PX MCA control' GUI (shown right) by double-clicking the 'PXMCA.exe' shortcut. Select the appropriate element then tick the 'MCA in coincidence' tick-box. A second program called 'PXPC142 MCB1' will then start up.
In this program, select 'Start' within the 'Aquire' menu, to collect the fluorescence signal. Check the peak starts to grow at the correct energy. With the 'Aquire' menu You can stop, clear and restart at any time.

The scan range is set when the element is chosen, but you can extend it if required.	If you choose an element other than selenium, you must ensure the lead plates at the end of the beamline do not block the beam.
Click Start Scan to collect the exafs data.

Problems	Solutions
The scan is a flat line at zero	There is no beam on your crystal or shutter closed or port closed or beam lost or beam misaligned or power supply off or lead plates cutting beam off.
The scan appears to be all noise	Ask the user support scientist to check the energy discriminators. Is there any Se in your crystal? Widen the scan range.
The scan is inverted: peak at lower energy	The fluorescence detector is overloaded. Reduce the counting time to 0.5 seconds or reduce the beam size or slide the detectors further away from the crystal.
The background level either side of the peak is similar	The fluorescence detector is overloaded. Reduce the counting time to 0.5 seconds or reduce the beam size or slide the detectors away from the crystal.
There is a discernible edge but it is noisy	The detector is not receiving enough counts. Increase the counting time to 2 seconds or check ion chamber reading is maximised or move the detectors towards the crystal.
There is an edge but it is towards one end of the scan range	Ask the user support scientist to check the monochromator calibration or change the scan range.