Chooch tips

Autochooch is now automatically executed when you perform an energy scan in MxCube and the values for the peak and inflection point energies are piped directy to the GUI and to the PX window. All the relevant AutoChooch files including a postscript plot of your edge scan as a function of X-ray energy are saved in the current directory (eg. "/data/bm16/external/mx333").

If you would like to rerun autochooch manually you can do it from the command prompt on bm16mach by typing:

PX> autochoochfordummies

However, for the Chooch affectionados who want to do it manually - all the possible options that can be invoked in chooch are listed by executing the following command

PX>chooch -h

If autochooch doesnt work or you dont trust the values given, you can still run chooch the old fashioned way by following the example given below (for a Se K edge scan);

PX> chooch -e Se -a K -p Se_K_1.ps -o Se_K_1.efs Se-scan.raw

The plot of the anomalous scattering factors as a function of energy will be written to the postscript file Se_K_1.ps and the data used to generate this plot are output to Se_K_1.efs. A typical edge scan for selenium is shown here.

Chooch is also installed on bm16process1 and can be run manually from there as outlined below.

To run Chooch simply cd to the directory containing your fluorescence data file (ex: se_edge.dat):

>cd /data/bm16/external/bm161###/

and type:

>chooch filename Element edge Number_of_points

(Number_of_points is usually 50)

Attention: filename must be entered without extension !!

Example:

>chooch se_edge Se k 50

Then follow these steps to analyse your scan:

1 - type "0". An horizontal line appears. Position it on the low level of your scan (corresponding to the low energies) by moving the mouse. Click with the left-hand mouse button.

2 - Do the step 1 once again for the high level (corresponding to the high energies).

3 - Confirm your selections by typing space 2 times. (or left-hand mouse button 2 times)

4 - Optional: a left-hand mouse click on the curve gives you the corresponding energy.

5 - Type "c" (continue). You obtain the first and second derivatives f 'and f '' curves. The energies for the peak and inflection points are displayed at the top of the window.

6 - Optional: type "p" to save the result in a postscript file (.ps)

7 - Type "q" to quit.

There is also an output on the terminal window where you can find f 'and f '' values for Emax and Einflexion.

If you want to print the result, type:

> lp filename.ps

in the terminal window. (ex: > lp Se_edge.ps)

A typical result for selenium is shown below: