Automatic Edge Scans
last modified
08-04-2010 10:24
- In an effort to standardise the beamlines (ID14-4 and ID29) we now use a similar procedure to ID29. All the Escan files for ID14-4 can be found in the "user defined scan" directory from mxCube. The days scans and autochooch files can be found in a subdirectory with the date, (eg. "/data/id14eh4/inhouse/Escans/22Jan2006"). The Escan (energy scans) are extremely poor quality and related to the energy movement problem noted above. We're working on the problem but it will not disappear in the near future. I have only used heavy atom solutions and was able to see a peak, so it remains to be seen how the beamline behaves with real samples. It is doubtful that chooch will work with these scans and the values should not be trusted and MUST be verified in newplot. To open newplot you need to log onto lid144 (ssh -X opid144@lid144). Then type 'newplot', scroll back in the EH4 spec session to the top of the Escan to see the file to where the scan is written and open it. The counter to look at is rtc1 (need to double check this). Please note the peak for SeMet should be 12.661 and the inflection should be 12.658. I would trust these values much above all others...
- NOTE - The automatic edge scans will now also try to move the undulators automatically or give a relevant message
- However it is always good to first check the undulator settings on the machine status window before starting to make sure that the U24.4 is either set to 19.6 mm (maximum intensity side-stations), 17.2 mm for Se, 21.2 mm for Br, 16.01 mm for As, Pt, Hg, W, or 18.7 mm for Pb. You have to change the gap if it is different from these numbers. Leave it at 19.6 mm if you found it like that and you've reasonable diffracting xtals with Se or Pb. Always inform the users of the other side stations first before changing the undulators, since this might effect their intensity. Advise them to do a quick-realign afterwards. Change the undulators only when really necessary => not more than 2 or 3 times per day.
- Select MAD as data collection mode and click on the element in the periodic to select the element of interest. Do Scan. You now have to wait patiently!
- Did the macro stop before doing the energy scan? This probably means that it could not find a proper attenuation factor. Check i) the beamintensity -storage ring, front-end, interlock, undulator settings, etc- and ii) whether the flouresence detector was moved in.
- Did the macro stop during the energy scan? Sometimes the mono does not feel happy. Just redo the scan, until you see the peak and the inflection point.
- Did you interrupt the scan? But why? Make sure that sample is still in the beam, e.g. by enabling the buttonbox - this will magically take care of it.
- Is the fluorescent scan very noisy? Make sure that the fluorescent detector is well aligned underneath the sample! If it was, then it probably means that too much attenuation was used. Use less attenuation. Type in the following command in the EH4-spec session: mcainit, mcaguion, mcaon, mattset N (N = smaller number than the one goven in PoDC), prodc_open_safety_shutter, open_ms_shutter, Escan E1 E2 100 1 (E1 and E2 are an energy 0.05 keV below and above the edge, and are given in keV) mcaoff and close_ms_shutter.
- Scan is completely flat. Note down your observation in the logbook, and redo the scan.
- You cannot find your edge. Ask you lc, (preferable in advance), to help to do it by hand if your edge is supported at all.
The macro will try to find the correct attenuation for the MCA, starting with the strongest attenuation in order to prevent unnecessary exposure of your precious sample. Provided that it found a setting that gave enough counts on the MCA, it will set the MCA parameters correctly, move the energy and will do the scan and displays the counter Normalised rtc1.
Open the scan file in the directory defined by the scan file and select the Normalised rtc1 from the scan using the program newplot on artemis and determine the inflection point and peak wavelength.
What can go wrong?