Lawrence Berkeley National Laboratory

Beamline Operating System (BOS) Manual

INTRODUCTION
CENTERING THE CRYSTAL
GETTING READY FOR DATA COLLECTION
TAKING A SNAPSHOT
STARTING A RUN
TAKING A FLUORESCENCE SCAN
THE MAD EXPERIMENT
DIFFERENT DATA COLLECTION STRATEGIES

Introduction

BOS is a software program used to control and operate Protein Crystallography
beamlines. It is currently used at beamlines 5.0.1, 5.0.2, 5.0.3, 8.2.1, and 8.2.2 at
the Advanced Light Source at Lawrence Berkeley National Laboratory. It was originally
based on the SSRL Blu-ice software, so that users from both facilities could move
between the two software packages with ease. It is currently being developed for offsite
data collection, so that users will no longer be required to travel to the synchrotron for
PX experiments.

Current features include:

Complete Redesign and Implementation of previous system

- Simple - Deterministic - Service Based
- Object Oriented
- RMI Based / SSL Compatible
- Robust and Reliable Device Architecture.

100% Java

- Runs on Linux/Sun/PC
- Leverages Java Tools - EJB,JBOSS,Tomcat
- Naming Service/ Implementation Repository

Database Independent

- All configuration based on XML files.
- DB may be used when available

New Flexible Jython based scheduler

- Robot Testing
- Tune-up scripts
- BOS console

 

Centering The Crystal

Note: We recommend that you start with an empty loop to familiarize yourself with the software
and to practice mounting crystals.

1. Move the collimator stage down by clicking on the Open Hutch button.
   Note: the stage will not move unless the hutch door is closed.
   
   
2. Open the door and mount the crystal (or empty loop) on the goniomter.
   
   
3. Close the hutch door and press Photons On button.
   
   
4. Click on the CENTER page within BOS (picture above).
   
   
5. Click on the sample using the LEFT mouse button. This moves the area clicked
   beneath the cross hairs and circle, which is the center of rotation. You may have to click
   a few times to bring the loop into the center of the screen.
   
   
6. Yoy can also center the crystal using the arrow buttons to the right of the image.
   
   
7. Click on +90 (or -90) to rotate the sample by 90 degrees, and center again.
   
   
8. Click on the Close Hutch button. This will move the collimator stage in and switch the
   view to the high-mag camera. Note: the hutch door must be closed in order to move the
   collimator.
   
   
9. Turn up the microscope backlight if necessary (LED slider to right of view).
   
   
10. Click on the sample to center it. Rotate the sample 90 degrees. Center again.
    
    
11. Check the alignment by rotating the sample by 180 degrees. The center of rotation of the
    loop sample should stay beneath the crosshairs.
    

 

Getting Ready for Data Collection

1. Click on the HUTCH page within BOS.
   
   
2. To change the detector distance, either type number into the box (in the picture above,
   the distance is 350) or click on the slide tab beneath the detector image. The distance
   will not change until you click on APPLY.
   
   
3. The resolution of the image corresponding to the detector distance you have chosen is
   shown by the red rings overlaying the detector image. In the picture above, the resolution
   at the edge of the detector is 2.4Å, and in the corner of the detector it is 1.8Å.
   
   
4. To move the detector to a 2-theta angle, either type a number into the box (in the picture
   above, the 2-theta angle is 0) or click on the slide tab to the left of the detector image.
   The detector angle will not change until you click on APPLY.
   
   
5. Change the wavelength by typing a number into the Wavelength box and clicking on the
   Apply button. Alternatively, you can type in an energy, such as 9500 eV.
   
   
6. The horizontal convergence is normally 2 mrad, as shown above in the box to the right of the
   wavelength. You can change this to a smaller value -- the result will be a reduction in flux
   hitting the crystal, and also a reduction in thesize of the diffraction spots on the image.
   
   
7. Note that changing the energy (eV), the wavelength (Å), the beam divergence (mrad), or the
   detector position (mm) or angle (degrees) will update the resolution rings on the image.
   
   
8. Click on any of the filters (Al, Cu or Se) to move them in or out of the beam path. You can use
   these to attenuate the beam if necessary.

 

Taking A Snapshot 

 

1. Assuming you have centered your crystal, click on the COLLECT tab within BOS
   (See picture above.)
   
   
2. Click on the 0 in the upper right hand corner. The zero indicates snapshot mode.
   
   
3. Set prefix and directory for the data files. The directory will be created if it does not
   already exist.
   
   
4. The default MODE is binned (2048x2048), 8 Mb per image (Q210 detector) or 18 Mb
   per image (Q315 detector).
   
   
5. Set the detector to desired distance from sample. Standard distances are
   150-500 mm.
   
   
6. Set collection time (in seconds), frame number, phi (angle of crystal in degrees),
   oscillation angle, and energy (in eV).
   
   
7. If you click on UPDATE button in the upper right hand corner the current values (detector
   distance, energy, angle) are read in. Do not hit UPDATE if you want to enter new values
   for the snapshot.
   
   
8. Make sure the hutch door is closed and the safety shutter is open.
   
   
9. Click on SNAP to take an image. The dark current is taken if the New Darks box is checked.
   
   
10. After the snapshot is taken, the image will appear in the workspace.
    
    
11. If the adxv viewer is not open, select Adxv Autoload or Restart adxv from the CCD pulldown
    menu.
    
    
12. Click on the image in the adxv viewer and hit H to autoscale. The scale and contrast can be
    set manually from the Adxv Control panel.
    
    
13. To see previous images (ie, not the current one), see Viewing Old Images.

 

Starting A Run     

1. Assuming you have centered your crystal, click on the COLLECT tab within BOS.
   
   
2. Click on the asterix to set up a run. Run 1 (indicated in the upper right corner) means
   you are in data-collection mode. Each time you click on the asterix the run number is
   updated. This way, you can set up several runs at once.
   
   
3. Set prefix and directory for the data files. Once you hit ENTER, the directory will be
   created if it does not already exist.
   
   
4. The default MODE is binned which is 8 Mb per image (Q210 detector) or 18 Mb per
   image (Q315 detector).
   
   
5. Set the detector to desired distance from sample. Standard distances are 150-350 mm.
   
   
6. Set the energy to collect data at. The maxium flux is at 1 A (12398 eV).
   
   
7. Set collection time (in seconds), oscillation angle, frame number, starting and ending phi
   (angle of crystal in degrees).
   
   
8. The resulting files will be listed in the middle panel. Adjusting the frame number and phi
   angles will update the list automatically.
   
   
9. If you click on UPDATE (upper right hand corner) the current values (detector distance,
   energy, angle) are read in. Do not hit UPDATE if you want to enter new values for the run.
   
   
10. Click start. A dark current is taken if the New Darks box is checked. Note that if the exposure
    time is very different than the previous exposure, the software will take a new dark shot whether
    or not the box is checked.
    
    
11. As the images are taken, they will appear in the window. If the adxv viewer is not open,
    select Adxv Autoload from the CCD pulldown menu.
    
    
12. Click on the image in the adxv viewer and hit H to autoscale. The scale and contrast can be
    set manually from the Adxv Control panel.
    
    
13. To see previous images (ie, not the current one), see Viewing Old Images.

Taking A Fluorescence Scan    

 

1. Make sure your sample is centered, the hutch door is closed, the "Photons On" button
   pressed, and the collimator stage is up.
   
   
2. On the scan page in BOS, select the edge you are trying to scan by clicking on the red
   K or L under the element. (When trying to decide which L-edge to use, keep in mind that the
   L3 gives the largest fluorescence signal.)
   
   
3. Enter your filename and directory in the appropriate fields.
   
   
4. There are two ways to do the scan:
   
   --Click the "Use Optimized Convergence" button and type in a value of 0.1. Make sure the
   "Optimize Fluorescence" button is not selected. This will not optimize the convergence
   setting;instead, it will start the scan using the convergence value that you typed in (0.1). In
   most cases,the convergence setting of 0.1 works well.
   
   --Click the "Optimize Fluorescence" button. Make sure the "Use Optimized Convergence"
   button is not selected. This will optimize the convergence setting before starting the scan.
   
   
5. Once the scan starts, the curve will be displayed.
   
   
6. Once the scan is done, you can analyze the curve using either Kramers-Kronig program
   or the Chooch program, as described below.

 

 

Kramers-Kronig

1. Open up a terminal window, and type kk to start the program.
   
   
2. Within the kk program, select File->Load scan.
   
   
3. The directories are listed in the left column.Double-click on each subdirectory until you
   reach the directory containing your scan file. Double-click on the filename to load it.
   
   
4. NOTE: if you have problems getting to the correct directory, exit the program and start
   it again. (The program gets easily confused if you do not double-click on the directory names.)
   
   
5. On the right side of the screen, select the absorbing element and click on AutoFit Curve.
   
   
6. To zoom in on the plot, click with the left mouse button, drag a box around the area of interest,
   and click again with the left mouse button. To zoom out, click once with the right mouse button.
   
   
7. Click with the middle mouse button and the energy corresponding to the position of the cursor
   will be displayed at the bottom of the screen, along with the f' and f" values at that point.
   

Find the maximum of the fluorescence scan (the f" curve) and the minimum from the f' curve (which should roughly correspond to the inflection point of the f" curve). These energies (plus a remote point ~300 eV above the edge) are the values to collect MAD data at.

Chooch

1. Copy the scan file to your home directory. For example, if you are in your home directory:
   cp /data/bl822/dcsuser/arnold/MyScan.scan .
   
   
2. Call Chooch and enter the scan file name, element of interest, and edge of interest
   chooch MyScan.scan Se K
   
   
3. The Kramers-Kronig plot should appear on the screen, along with the f' and f" values at the peak
   and inflection point.
   
   
4. NOTE: Chooch will output several files:.efs contains the rawdata for the splinor fitted data used
   to make the gnuplot.inf contains the chosen f' and f" values and the associated anomalous
   scattering factors.ps is a postscript file of the gnuplot
   
   
5. ANOTHER NOTE: The fluorescence scan requirements for using chooch are very specific.
   If these requirements are not met you should not trust the results:
   ---The background scatter must be low and vary slowly and smoothly with energy
   ---The scan data must be measured starting 200 eV below the absorption edge to 200 eV above
   the absorption peak.

 

The MAD Experiment     

(Assuming the crystal is already mounted and centered)

1. Click on the COLLECT tab in BOS.
   
   
2. Click on the asterix to setup a run. Run 1 (indicated in the upper right corner) means you are in
   data-collection mode.
   
   
3. Set prefix and directory for the data files. The directory will be created if it does not already exist.
   
   
4. The default MODE is binned which is 8 Mb per image (Q210 detector) or 18 Mb per image
   (Q315 detector).
   
   
5. Set the detector to the desired distance from sample. Standard distances are 150-500 mm.
   
   
6. From the fluorescence scan, you should know the energies for data collection: the minimum of the
   f' curve (which corresponds to near the inflection point of the fluorescence scan), and the peak of
   the f" (fluorescence) curve. For example, for Se usually f'~12.662 KeVand f" ~12.658 keV. The
   remote energy is generally choosen to be ~50-300 eV above the peak.
   
   
7. You can set up a single run to collect several energies by typing the energies into the boxes.
   Alternatively, you can set up Run1 and one energy, Run2 at another energy...etc. See the
   different data collection strategies below.
   
   
8. Set collection time (in seconds), oscillation angle, frame number, starting and ending phi
   (angle of crystal in degrees).
   
   
9. The resulting files will be listed in the middle panel. Adjusting the frame number and phi angles
   will update the list automatically.
   
   
10. If you click on UPDATE (upper right hand corner) the current values (detector distance, energy, angle)
    are read in. Do not hit UPDATE if you want to enter new values for the run.
    
    
11. Click start. The dark current is taken if the New Darks box is checked.
    
    
12. Only the current image is displayed in the window. To see previous images (ie, not the current one), see
    Viewing Old Images.
    
    
    

Different Data Collection Strategies

1. Collect one wavelenth at a time, with inverse beam, in 20-30 wedges. Collect the f"; (peak) first,
   then f' (inflection), and finally the remote wavelength.
   
   
2. Collect the inflection and remote wavelengths at the same time, interleaving the inflection and
   remote energies (no inverse beam). Then, collect the peak.
   
   
3. Collect all wavelengths at once, interleaving the energies, with a wedge size of one.The staff will
   be happy to discuss the pros and cons of the different data collection strategies above.
   
   
   

Viewing Old Images

1. You can open the program ADXV one of two ways:
   
   click on the ADXV icon on the desktop
   or, open a terminal window and type adxv at the prompt.
   
   
2. Under the Adxv Load panel, type the directory name containing the file you wish to view.
   Normally the images are stored in /data/dcsuser/groupname. Click List to see the files.
   Double-click on a file to select it and bring up the image.
   
   
3. Move the cursor into the image space and hit H to autoscale. The scale and contrast can be set
   manually from the Adxv Control panel.
   
   
4. Right-click within the image to open up a magnified view. You can move the magnified
   window around by holding down the right mouse buttom while moving the mouse.
   
   
5. Left-click on the image for a line profile.
   
   
6. Middle-click to drag the image around within the screen.
   
   
7. Move the cursor into the image space and hit H to autoscale. The scale and contrast can be
   set manually from the Adxv Control panel.