Home | Site Map | Facilities | User Guide | Schedule | Forms | Research | News | Staff | Links

Collect Tab

The Collect Tab is used for collecting test images and complete monochromatic, SAD and MAD data sets. Multiple run windows can be set up by creating additional Run Tabs.

Data collection runs

  • Run tab 0 is dedicated for taking single test images in order to test crystals and plan strategies for data collection. Consecutive images cannot be collected from this run. A resolution predictor widget displaying the resolution limits for use input values of the detector and beamstop position and energy is available in this run.
  • To create additional data collection run, click on the '*' tab below the '0' tab. Runs numbered 1 and above can be used to collect complete data sets at multiple energies. Note: When you create a new "run", the contents of the old run are automatically copied to the new run.
  • An alternative way to collect test shots and generate data collection runs is by using the Web-Ice strategy calculation. To access this tool, click the Web-Ice Strategy button. This will open a browser and start Web-Ice. See the Web-Ice documentation. Note: Data collection runs exported from Web-Ice can be paused, reset, modified or aborted from Blu-Ice.

Data collection parameters and commands

Click on the links above for information on each parameter or input window.

  • A motor or parameter value displayed in red indicates that the motor is in a different position. The motor will move the position in red upon starting data collection.
  • If you click on Default, the current values of distance, axis and energy will be selected and displayed. In addition, prefix will be set to 'xtal', directory to '/data/username'. The default detector mode, delta phi and exposure time are different for each beamline.
  • Click on Update if you wish to use the current motor positions for the data collection. This is useful if you have already set up the correct detector or beamstop distance from the Hutch Tab. If you have mounted a sample using the screening tab, update will also change the directory and image prefix names to the ones defined in the screening tab. Similarly, if you have done a MAD scan in the Scan Tab, the optimal energies for a MAD experiment will be copied to the run.

    • Important: Do NOT click on the Update button once you have finished editing the collection run. This will cancel all your edits.

  • Use the Delete button to delete the run that you are in. You cannot delete Run 0. Be careful when using this command. Once a run is deleted, you cannot return to it.
  • Use the Reset button to re-use a run. If you do this you should change the image name or the destination directory. If you do not change the names, Blu-Ice will create a subdirectory called OVERWRITTEN_FILES where the old files will be stored. This will protect the images from one accidental overwrite.
  • Another use of the Reset button is to edit data collection parameters after stopping a started run (for instance, to change the detector position). Note: if you click "Collect" immediately after editing the run, data collection will restart on the first image again. In order to continue collection at the current frame, double-click on the image name as explained in the Tips.


prefix
  • Filename root or file prefix
directory
  • Shows the directory in which the image will be saved. Note that only directory paths starting with "/data" are allowed.
detector
  • Specific values for the detector depends on the type of detectors. SSRL beamlines use Q315 and MAR325 CCD detectors. Q4 and MAR image plates are still supported, but not in regular use on any user beamlines.
  • The ADSC Q315 detector can be used in "binned" and "binned dezing" modes. Unbinned images are not supported (they are 4 times the size at no significant gain in spatial resolution on a typical SSRL beamline)
  • In "dezinger" mode two images are collected with half the entered exposure time and the pixel values for each image are compared. If one pixel is a zinger, instead of using this pixel from this image, the software doubles the corresponding pixel value for the other image. Otherwise, the pixel values for both images are added to produce a final image.
  • Use dezinger mode if your exposure time is greater than 20-30 seconds.
  • The MAR325 detector can be used in "normal" and "dezingered" modes.
  • The Q4 detector has 4 modes: slow, fast, slow dezinger, fast dezinger. We recommend slow or slow dezinger.
    • Fast takes 6 seconds and is accurate to 14 bits.
    • Slow takes 10 seconds and is accurate to 16 bits.
  • For information on mar IP detector modes consult the mar345 IP page.
distance
  • Distance between detector and sample in millimeters; the minimum distance is usually between 90 and 110 mm, depending on the beamline.
beamstop
  • Beamstop distance in millimeters. The optimal beamstop to sample distance can be determined with Web-Ice
attenuation
  • Beam attenuation. Use to avoid overloaded spots when collecting low or medium resolution data from strongly diffracting crystals. Note that in general you should never change the attenuation (whether manually or within the run) after normalizing the dose.
axis
  • Phi is usually used.
  • When Kappa is not set to zero, you must collect using Omega.
  • The rotation range of Omega is limited.
  • Omega and Kappa are usually locked to prevent hardware collisions, but can be unlocked if the experiment requires it: contact your support staff.
delta
  • Oscillation length per image.
time
  • Length of exposure time in seconds. It is strongly recommended to use Web-Ice to estimate the optimal value. Note that if you change the oscillation angle per image, the exposure time should be changed by the same factor to obtain an equivalent exposure per image.
start
  • The number and phi value assigned to the first image.
end
  • The number and phi value assigned to the final image.
inverse beam
  • Rotates the crystal by 180 deg to collect the Friedel pairs for the input phi range.
  • When inverse beam is used for a MAD experiment, the inverse beam pass is collected before changing the energy.
wedge
  • The phi rotation range that is collected consecutively before rotating the crystal by 180 degrees (with inverse beam) or changing energy (during Multi-wavelength experiments).
energy
  • Energy or energies used for the experiment. As you enter an energy value, an empty box appears for further energy entries. The energy boxes can be auto-filled by clicking on the Update button after doing a MAD scan. If you wish the skip one or two of the selected energies, simple delete the value.

Dose Mode

    Dose mode is the optimal way to collect diffraction data with a decaying or fluctuating X-ray beam. The data collection process is controlled by the following equation. 
        Real exposure time = exposure time (sec) x Dose factor
    Multiplication of the exposure time (entered in the box in the collect tab) by the dose factor ensures that all the images receive approximately the same X-ray dose. Although the final measured diffracted intensity may vary between frames owing to different x-ray absorption at different orientations of the crystal, use of the dose mode prevents abrupt scale changes between contiguous frames and compensates for oscillations of the beam intensity.

Note that once dose mode is selected, the setting will apply to all the images collected in subsequent runs and also from the screening tab.

When to use dose mode

    Dose mode is particularly useful for:

    • Long data collections stretching over more than one hour (about 20 or more seconds per frame)
    • MAD data collections:it ensures that data sets collected at different energies are approximately on a similar scale (this is true as long as the energies do not differ by more than ~1000 eV).
    • It is not necessary to use dose mode to prevent the collection of blank images in case of beam loss. The control system automatically checks and waits for the spear status and expected ion chamber readings before collecting a new image, regardless of dose/time mode.

Dose factor calculation

    The dose factor is calculated by dividing the reading from the second ion chamber when the dose was last normalized (Io) by the reading at the start of each successive frame exposure. For example, if at frame number n the second ion chamber reads In , the dose factor for that image will be: 

            Dose factor = Io/In

    The dose factor and real exposure time for each image are displayed by Blu-Ice next to the entered exposure time. Important! Note that, unlike the MAR software, Blu-Ice does not calculate a dose factor per degree. So, if you change delta phi between data collection runs of the same crystal, you must edit the exposure time in the box and change it by the same proportion.

Normalizing the dose factor

    The normalization button under the dose mode check button is used to store a new "Io" value and reset the dose factor to 1. This must be done after you 1) determine the correct exposure time, 2) adjust the beam size, attenuation and energy to the starting values in the data collection run, and 3) optimize the beam. Normalizing the dose before the data collection software automatically moves the energy or attenuation can lead to undesired long or short exposure times.

    In normal circumstances, you should never press the normalization button again until you change crystal. If you have to change the exposure time (for example, if you get overloaded spots at a certain orientation or you change the beam size) you can enter a different exposure time instead.

    Consult support staff if you have any doubts whether to normalize the dose factor or not.

Starting a Data Collection Run

  • After setting all parameters to your desired values click Start to collect an image.
  • The network status of your Blu-Ice Client must be Active to collect an image.
  • If you have created a few runs and start data collection from a previous "run", Blu-Ice will collect frames from the current run and the following runs (Note: Blu-Ice will not recollect frames from an already completed "run"). This allows users to collect multiple data sets (eg., low resolution pass, high resolution pass or different wavelengths) using different "run" windows.

Data File Naming

  • Each data file in your selected run sequence is named in the following way: 'file prefix'_'run number'_'energy number'_'image number'.img.
  • For example, a file could be named data_2_E2_010.img. This image is in the 10th frame collected in Run 2 at the 2nd input energy.
  • With only one energy level selected, the file would be name 'file prefix'_'run number'_'image number'.img.

Run Sequence

  • The run sequence depends on the values for phi, wedge, energy or inverse beam that you choose. The image collection order will be displayed in the 'run sequence' window. Below are examples of some possible run sequences.
  • Note: Once the current run is finished, the software will go on to collect any unfinished runs following the current one.

    One Energy, Inverse Beam Off,
    Phi < Wedge Size
    (simplest case)
    example:
    test_1_001
    test_1_002 
    test_1_003
    (phi: 0-3 deg, wedge: 5 deg, 1 energy, inverse beam off)
    Two or more Energies, Inverse Beam Off, Phi < Wedge Size

    example:
    test_1_E1_001
    test_1_E1_002
    test_1_E1_003
    test_1_E2_001
    test_1_E2_002
    test_1_E2_003
    (phi: 0-3 deg, wedge: 5 deg, 2 energies, inverse beam off)
    Two or more Energies, Inverse Beam On, Phi < Wedge Size

    example:
    test_1_E1_001
    test_1_E1_002
    test_1_E1_003
    test_1_E1_181
    test_1_E1_182
    test_1_E1_183
    test_1_E2_001
    test_1_E2_002
    test_1_E2_003
    test_1_E2_181
    test_1_E2_182
    test_1_E2_183
    (phi: 0-3 deg, wedge: 5 deg, 2 energies, inverse beam on)
    Two or more Energies, Inverse Beam On, Phi > Wedge Size

    example:
    test_1_E1_001
    test_1_E1_002
    test_1_E1_181
    test_1_E1_182
    test_1_E2_001
    test_1_E2_002
    test_1_E2_181
    test_1_E2_182
    test_1_E1_003
    test_1_E1_183
    test_1_E2_003
    test_1_E2_183
    (phi: 0 - 3 deg, wedge: 2 deg, 2 energies, inverse beam on)

Image display commands

New images are displayed to the left of the collect tab as soon as they are written to the users' area. Older images can be displayed and inspected by launching the web-browser based Image Viewer in Web-Ice or the program ADXV.

brightness
  • The default image Brightness value is set to 400. Change this value for a desirable contrast between spots and background.
zoom
  • Click on this to zoom in or out of the diffraction image.
move arrows
  • Pans the image within the display box.
Alternative image viewers
  • Allows the user to inspect and analyze diffraction images with Web-Ice or ADXV.

Useful Tips

  • Subdirectories are automatically created.
  • The asterisk (*) in the 'Run Sequence' box is always adjacent to the next image to be collected. You can jump to a different image if you double click on the desired image name. You will notice that the asterisk moves.
  • Pressing the "Pause" button stops the data collection after completing the current frame and pressing the "Abort" button immediately stops the data collection.
  • Double-clicking on an image automatically starts ADXV.