How to Start the Experiment on F2

For MAD runs, the station monochromator is set (by CHESS staff) at the absorption edge of the appropriate element. Energy scans may be easily performed in the vicinity of this energy. A reference sample containing a high concentration of the element is provided in front of the shutter box. This sample may be rotated in and out of the beam, and energy scans may be done on it, for the purpose of checking the x-ray energy. A second fluorescence detector is provided for doing energy scans on your crystal. Such a scan is used to set the exact energies at which data will be taken.


	Station computers

On the data collection computer:
	log in as "specuser", if necessary, the password is available from the CHESS and MacCHESS personnel;
	check the disk space available for data collection and create the directory with PI's name;
	type "start_ccd" in the terminal window;
	two windows, "ADX" and "ADX-Status", will appear.


On the hardware control computer:
	log in, if necessary, as "specuser" using the same password;
	press the "MacCHESS" icon to start "OpsTerm@f2.chess.cornell.edu" and "CHESS spec functions", each on its own window.


Make sure there is a beam passing through the collimator.
In the "OpsTerm@f2 window" type:
	opens - to check the counts by opening the shutter in front of the collimator;
	closes - to close the shutter;
	if counts are low, align the optical table using the "Quick Table Alignment" button on the "CHESS spec functions" window.


In the "CHESS spec functions window" use:
	Quick Table Alignment - this is the alignment to use in most cases. Make fine adjustments to the optical table to align the collimator with the beam and to maximize counts through the collimator. If counts do not return to previous value, call CHESS operator for help. If you are getting the messages "define_table" or "set_table_zero", follow the instructions and press "Define Table" or "Set Table Zero" buttons found in the "CHESS spec functions" window. Equivalently, you may type command "quick_align" in the "OpsTerm@f2" window.
	Set Table Zero - this must be done whenever the motors that control the table position have been moved for some reason, i.e. not through "align_table" or "quick_align" macros. This command defines the current optical table position to be the zero position.
	Define table - enter optical table parameters. You will be asked for parameters. Normally, you will accept the default (standard table) values. Press OK.
	Interrupt Spec - stops motor motions immediately and returns to the original position. Equivalent to typing "abort" in the "OpsTerm@f2" window.


	MAD setup

	Open MAD setup page and check all the commands for the MAD setup.
	madsetup command - enables you to enter MAD parameters, under this menu you are able to:
		r - alter reference scan parameters and set the energy range;
		c - alter crystal scan parameters and set the energy range;
		check the energy range for refscan and xtal_scan to be the same.


Reference scan:
	refscan command - rotates the reference sample into the x-ray beam, scan the energy over the range you gave it in madsetup, and both list and plot the resulting x-ray fluorescence on the hardware control computer screen; the energy is reset and the sample is rotated back out of the beam. On the reference scan, note the energy of the peak (or whatever spectral feature you plan to monitor). During the experiment, if this energy ever drifts by more than 2 eVs, you will want to adjust the calibration of the mono so that it returns to the original energy value. To make the adjustment, use the following rspec/OSCAM commands:
		moveE ### - where ### is the energy at which OSCAM thinks the selected feature (e.g. the inflection point of the edge or the peak of the white line) occurs;
		setE ### - where ### is the true energy for the feature (inflection point of the edge or the peak of the white line);
		refscan - check if E has the value equal to the set E### value; if not - repeat the calibration.

Perform refscan occasionally to check if the energy is stable!

	Crystal centering

On the station computer (A1 & F1, or Guideline for F2) open terminal window and type "start_centering" to bring up automatic crystal centering program:
	double click on the crystal in order to bring the crystal to the crosshair;
	rotate the spindle 90 degrees and double click on the crystal again and so on;
	rotate the crystal 360 degrees to insure perfect centering.

If you have problems centering the crystal, please go to "Crystal centering problems"

Crystal scan.
The crystal scan need only be done at the beginning of the experiment. For the crystal scan use a crystal that you are willing to heavily expose. It should be as large as possible, and does not have to be single. In order to get a good signal-to-noise ratio, the fluorescence detector should be placed at 90 degrees to the beam, i.e. pointing along the spindle axis. Now, with new cold stream setup, it is possible to perform crystal scan on frozen crystal. Scan the crystal over the range you gave it in madsetup (the same range as for energy scan) and look for both list and plot the resulting x-ray fluorescence on the hardware control computer.
	xtal_scan command - runs the scan, using the parameters from madsetup;
	repeat until you have a reasonable fluorescence scan;
	run refscan immediately before and after the final crystal scan;
	compare the peaks (or some other features) of both reference scans to verify that the mono did not drift; if it drifted 1 eV or less, then select your desired wavelengths from the crystal scan.


For a 3-energy experiment use:
	the top of the "white line" peak;
	the inflection point of the edge;
	the point about 200 eV above the edge.

For a 4-energy experiment, use the point slightly below the edge as well.

If the calibration is successful, set the desire wavelength on "Oscam" terminal window *:

	moveE ### - where ### is your desired wavelength from the crystal scan;
	getE - to check the current wavelength.

*This is the old version (manual) for changing the wave length, see bellow for the new method.

Raise the safety shield in front of the CCD after you close the hutch door:

	press the black button on the control panel and make sure green "Garage door" light is on;
	if the shield does not move, check:
		if there is a beam through the collimator;
		if the beam stop is in place;

Remember to raise the safety shield every time you close the door in the hutch!

Data collection

Project setup (optional): on data collection software program use Setup/Project to enter file names, etc. ADX will create a subdirectory for you, if necessary, but not multiple levels of directories.

Snapshot Mode: use Setup/Snapshot to take a test exposure from your crystal. Take more exposures, if necessary, to optimize the data collection parameters:

	make sure you tell the program to take a new dark current with the exposure time that you have selected;
	the first snapshot will start up an ADXV display process; for display of multiple snapshots keep ADXV running;
	rotate the crystal by entering a new phi value;
	set direct beam position parameters:
		press Edit/Settings;
		enter approximate coordinates for x and y in the appropriate fields if you do not see the cross on the screen;
		use arrows for fine adjustment of the direct beam center position;
	to view the resolution rings:
		press "Resolution rings On" (make sure the CCD distance is correct).

Run Mode: data collection is normally conducted through the "Run" window (press Setup/Run(s)):

	for normal data collection in ADX control panel use the "Display" button to turn on the "Follow images" mode, if you do not already have an "ADXV" window;
	check the directory;
	set data collection parameters;
	set an "Anomalous" option by choosing "Yes", if you collecting data with the inverse beam;
	select "MAD" for Mad data collection * * ;
	set the desired wavelengths in the "Mad" window and select "Each Run" bellow;
	check the direct beam position parameters;
	start collecting data by activating the "Collect" button;
	the program starts the data collection by taking the new dark current image automatically and retakes the background image (optional) every certain period of time (7200 seconds), set this up in "CCD Config" window (press Config/CCD).


**This is the new version of changing a wave length, controlled by data collection program:
	In the "MAD" window check mark the first wave length and uncheck the others. In this case the program will collect the data set only at marked wave length. Once you finish the first data set, you can switch to the second energy, adjust the parameters in the "Run" window (set the next run number) and so on. This way the software will control the mono movement from one energy to another.
	If you decide on the different strategy, for example, you want to collect data on multi wavelength at once, all wave lengths should be check marked and only one line of parameters should appear in the Run widow. Also, make sure "Each Run" option is on.

Data files are corrected while subsequent images are being recorded, and corrected files may be processed during data collection with minimal effect on running. Raw images are saved by default, but if you do not need them:
	open "CCD Config" window (press Config/CCD);
	uncheck "save raw images" option.

The "ADX Status" window shows the current image name, spindle angle, and CCD distance.

To interrupt the data collection:

use the ADX control panel function "Stop/After Current Image" and let the oscillation end;

To resume the data collection

	in the "Run" window click on "Restart", a new window will appear in which you can enter the Run # and the Frame # at which you wish to restart;
	if you give a value lower than the current frame, data files will be deleted so that there is no duplication of files;
	click OK in the "Restart" window;

When a run is complete, you can start another by setting parameters in the "Run" window and activating "Collect". For a new crystal, repeat from step "Mount and center a crystal".

To terminate programs:

type "stop_ccd" in any window, this stops all processes on collection computer.

See the Troubleshooting guide if you have any problems. Call CHESS operator for help.

Last updated August, 2006

How to start the experiment on F2