Configuring the Source Beam With IMCAGui

Starting imcagui

Overview of imcagui

Menu Bar

Energy Block

Harmonic and Mirror Block

Servo Block

Slit Block

Attenuator Block

Optimize Block

Message Log Window

Setting the energy (wavelength)

Tuning the monochromator

Detuning

Defining beam size and slit position

Aligning the mardtb to the beam

Summary

Troubleshoot

Starting imcagui

The program used to control the beam-line hardware for crystallography is called imcagui.  This software is only in use on 5ID-B and is run from banana1.  To run this software log in as maruser, open a shell window, and type:

imcagui

This will open a small text window and after a few moments the main imcagui window will appear

Overview of imcagui

This is the main imcagui window

As a general rule of thumb, blue text and green buttons are good: they generally indicate that there is nothing too unusual.  Generally yellow text means that thing is moving; and red text, orange text, and/or pink buttons indicate that you may want to confirm that the beam-line is configured how you want before you proceed with data collection.

Menu Bar

From the menu bar you can control various parameters and start MAD experiments among other things.  Here is a summary of the functions

File

Edit

Variables

allows you to change certain beam-line configuration variables to change the behavior of the controls

Experiment

Help

Energy Block


This block is used to set the energy (wavelength).  The energy is set by typing desired energy or wavelength in one of the entry boxes at the top of the main window and then clicking the "Move" button.  This will cause both the undulator and the monochromator to move to the desired energy. 

The "Gap Energy" refers to the energy reported by the undulator insertion device at a given gap setting.  This energy should be slightly larger (~ 100-400 eV) than the energy reported by the monochromator (the top value).  This is because there is an offset between the energy reported by the undulator and the energy with the most flux for any given gap setting.

Harmonic and Mirror Block


This block displays the current harmonic used to convert the undulator gap setting to the reported energy.  All the harmonics are always produced (although the odd harmonics tend to be more intense), the harmonic variable just determines what energy is reported for a given gap setting.

This block also displays the status of the mirrors.  Whether they are "Out," "Rh in," or "glass in."  If you are using mirrors (which is usually the case for crystallography), The mirrors should be on the

Servo Block


This block shows the status and allows for control of the servo. 

"Tune" is the current value of for the second crystal rotation (also known as mono_coil).  This motor is adjusted to maintain a constant position as monitored in 5ID-B by the position monitor.

"Servo Lock" displays the status of the control loop.  Normal modes are "Locked In", "Correcting", and (when the A or B shutter is closed) "Intensity Too Low"

The button is a toggle button which enables and disables the control loop.  When the servo is first enabled, it has to measure the dark current.  To do this it closes the PF2S2 shutter.  So you will see no intensity on the mardtb ion chambers while this is happening.  Dark current measurement lasts a few seconds and the status is shown as "Get Dark Current"  After this it will take another few seconds for the servo to create a new set-point from the current position.  The status will be shown as "Get Setpoint".  Finally the servo should display "Locked In".

It is important to realize that toggling the servo off and on will cause it to find a new set-point for whatever position it is at.  For this reason it is best to optimize the tune prior to enabling the servo.

Slit Block   


This block shows the current size of the beam-defining slits.  From here you can change you beam size based on the size of your crystals.  Normally we run at 200 µm, and it is not advisable to go much below 100 µm as the matdtb spindle alignment is only good to ±50 µm.

Attenuator Block


This controls how much Al foil you put in to attenuate the beam.  You should not have to attenuate for normal data collection.  However, when you are doing a fluorescence scan it is usually necessary to prevent overloading the detector.

Optimize Block


This will open the Optimize GUI to manual optimize both the tune and the beam-defining slit positions.

Message Log Window


This window shows a running log of what you are doing.  It is useful for diagnosing problems when there is an error.  Scan data also appears here, so it is useful for picking out individual points of a scan.

Setting the energy (wavelength)

The energy is set by typing desired energy or wavelength in one of the entry boxes at the top of the main window and then clicking the "Move" button.  This will cause both the undulator and the monochromator to move to the desired energy. 

Several variables control how a move command affects the insertion device.  If ID_ev_enabled is set to 0, only the monochromator will move.  If ID_ev_s_enabled is set to 1 the undulator will automatically switch harmonics between 1 and 3 depending on the desired energy.  See the variables section above for more information.

Tuning the monochromator

Choosing "Manually Optimize..." from the "Optimize Intensity..." button will bring up the following window:

From here you can tune the monochromator by clicking the "Optimize Tune" button.  This will do a scan and plot the tuning curve. 

Any time the energy is changed by more than 1000 eV or so, you should re-optimize the tune.

Detuning

After tuning the crystal the Monochromator block of the Optimize GUI should look similar to this:

If you are not using the mirrors (look at the imcagui mirror block if you are not sure), you will probably want to detune.  After optimizing the tune, the "Detune" button will become active and allow you to move the tuning crystal to a position calculated based on the curve fitting and the detune variables you have defined.  These variables will allow you to decide what fraction of the peak height is used to determine the tune position, and which side of the tuning curve to be on.

As of October 2002, we have a position monitor in 5ID-D that is used for servo control.  For this reason you do not have to detune unless you are not using mirrors.  The servo adjusts the tune motor based on a linear function representing position rather than on a linear region of the tuning curve itself.  This means that it can lock on any part of the tuning curve.

Defining beam size and slit position

The beam size is chosen prior to optimization.  You can change the size in both the vertical and the horizontal in the slit block of the main imcagui window.  Normally we run at 200 µm, and it is not advisable to go much below 100 µm as the matdtb spindle alignment is only good to ±50 µm.

The position of the slits are not directly controlled, but rather are set to an optimum position as the result of a scan.  This is done from the Optimize GUI and the procedure is the same as for optimizing the tune.  Click first on the "Optimize Vertical Slit" button and then after it is complete (plotting, curve fitting, and selection), click on the "Optimize Horizontal Slit" button. 

If either the vertical or horizontal positions change by more than 2 times the slit size, you might want to go back and optimize again (iterate until the position change is less than 2 times the slit size).  After optimization, the Slits block of the Optimize GUI should look similar to this:

Once the Monochromator tune and the Slit positions are optimized, you can either dismiss the Optimize GUI or leave it up for the next time you change the energy by more than 1000 eV or so.  Any time you change the tune position, you should re-optimize the slit position.  You should not have to re-optimize after making the slit size larger, but you might want to if you make the slits smaller.

Aligning the mardtb to the beam

The mardtb can be aligned to the beam fairly simply using the software from marresearch.  This software is run from prune1, the data collection computer.  However in order to run this software, you can not be running marccd.  After the tune and slit positions have been optimized and the size defined, the steps to aligning the mardtb to the beam are as follows:

The alignment procedure will then do four separate scans.  With the first two scans, the procedure will find the peak intensity in Chamber 1 (behind the first set of slits) for horizontal and vertical translations.  With the second two, it will find the peak intensity in Chamber 2 (behind the second set of slits) for horizontal and vertical rotations (with the center of rotation being the first set of slits). 

An example of each of these scans is shown here:

Each of the plots should be linear up to a sharp peak and then linear back down again.  If the top is a plateau, then the slits on the mardtb are not the same size as the beam-defining slits.  If this is the case, you may need to re-initialize the slits.  See the marccd software section of the data collection resource page for more information on initializing motors with marccd.

Once the mardtb is aligned click the "Quit" button in the main "strip" window.  This will exit mardtb.  Be sure to quit mar345dtb before re-starting marccd!!!

Summary

Here is a summary of the steps uses need to perform to prepare the undulator beam for macromolecular crystallography in 5ID-B.  To be safe, you (or a staff member) should go through these steps at the start of your time, and then as your experiment dictates.  All but the last step are done using imcagui on banana1.

Troubleshoot