Helical Collect Tab

The Helical Tab allows collection of oscillation data while translating the crystal along the spindle axis: The software collects one oscillation image before moving the crystal to a new position and collecting a new image, with the new oscillation starting where the previous one ended.

While in general, the best strategy to minimize radiation damage is to collect from the largest possible volume of the crystal, the helical data collection is advantageous when the crystals are larger than the beam in the horizontal (spindle) direction, or when the crystals are inhomogeneous and the diffraction quality varies along their length. If the beam size at the beamline can be set to the crystal size and you wish to minimize radiation damage, *DO NOT* use helical data collection as the diffracted intensity/dose ratio is maximum when the beam size matches the crystal size!

The Blu-Ice interface makes it possible to define the translation axis along the crystal and the size of the beam (FWHM), as well as other data collection parameters such as the oscillation range per image and the exposure time/attenuation per image.

Helical Collection Tab Widgets

[Figure 1] Helical Collect tab

When clicking on the helical collect tab, Blu-Ice displays several default windows or widgets, the Helical Collect and the Heads-up Display are used to define the data collection run, while the Diffraction Image View and Collect Frame View are used to monitor the data collection itself. Other functions and tools tab can be selected from the Individual Widget drop down menu shown in Figure 2. You can save a different widget set to the default and reload them for use in future experiments using the Save Widgets Layout and Load Widgets Layout buttons.

[Figure 2] Widget selection

Defining the Helical Collection Path

The Helical data collection starts by defining the section of the crystal for helical data collection using the define new crystal button in the "Heads-up Display-Inline View" (available on BL12-2) or the "Heads-up Display - Sample View". The interface displays a message describing the process to select the two ends of the crystal for helical data collection (Figure 3). The first step is to define one end of the crystal by centering that end in the beam, using the Sample Positioning Tools described in the Sample Tab: Click-to-center the sample at two orientations 90 degrees apart) and then clicking the Save button (Figure 3, left panel). In the second step, the same process is repeated for the other end of the crystal. (Figure 3, right panel).

[Figure 3] Helical collect (defining start of helical path

Helical Collect (defining end of helical path)

Once the second point is saved, the software draws a white line joining both points, which indicates the helical collection axis, and blue boxes at the different positions at which data will be collected. The number and distance between the boxes is determined by the distance between the start and end points and the current beam size, and their size is equal to the size of the beam as seen from the camera -ie, when the blue box turns into a line, it means that the crystal will be rotated 90 degrees at that position. The position of the start and end points can be changed by clicking on the Modify button; the beam size and phi position can be changed in the Helical Collect widget. If you want to start over, use the Delete button.

  • If you wish to click-to-center the crystal without defining a helical path, tick the Align Visually box to the right of the "Modify" box.
  • The current beam size and position is shown as a white box, and the beam center is indicated by the intersection of the two red lines across the video display. The Show beam menu in Display options can be used to hide either or both.
  • The length of the helical collection axis can be changed by left-clicking either end of the line and dragging it with the mouse to the desired position. Left-clicking elsewhere on the line, will allow translation of the entire line.
  • The helical path can also be modified with the positioning tools above the video display (see Figure 4).

[Figure 4] Positioning tools to modify the helical path: The input box defines the distance by which the position or lengths will be changed. A new number can be selected with the drop down menu or entered in manually; The single arrows translate the line by the given distance in the direction of the arrow. The double arrows expand or shrink the line length.

Defining the Helical Collection Path using Raster Tab Results

When it is difficult to see the crystal in the sample mount or the crystal is split or highly mosaic, one may need to use low dose X-ray rastering to locate the crystal or its well diffracting portions before defining the helical collection path. The raster tab can be used for this purpose:

  • From the raster tab, do a 2D plane raster. Center one end of the crystal in the beam (either by clicking twice on the display or once in the node in the raster list). Then do a 1D (line) raster +90 degrees away around that position as documented in the raster tab instructions.
  • After the line scan is finished, rotate the sample -90 degrees to see the 2D scan again and center the other end of the crystal. Then repeat the line scan +90 degrees away about the second point.
  • Go to the Helical Tab and click Show rasters in the Heads-up display. The two line rasters will be shown.
  • Click on the starting point for the helical data collection, then rotate the crystal by -90 degrees to show the 2D scan, click to center on the starting point in that direction and then click the Save button. Repeat the procedure for the end point.

See also this document for an illustrated description of the above procedure.

Defining the Helical Collection Parameters

As soon as the crystal is defined, a new run is created for the selected crystal in the "Helical Collect" widget (Figure 3). This widget is used to select the image file prefix and directory and the collection parameters, such as the detector and beam stop distances, energy, attentuation and exposure time, and start and end file. There is also an option to change the selected collimator (on BL12-2) and the beam size. Once the helical run is defined, the data collection can be started and stopped with the Start and Pause buttons.

[Figure 5] Helical Collect widget
  • The Default and Update buttons and most of the collection parameters function as described in the Collect Tab. "Update" will usually move the parameter values to their current position, while "Default" will select default values for the attenuation, exposure time and oscillation range. Suitable values for the detector and beamstop distance, exposure time per image and attenuation, oscillation per image and start and end phi can be obtained from Web-ice, which can be launched with the Web-Ice Strategy button.
  • The Beam size (horizontal, vertical) for data collection will default to the current values, but it can be changed using the drop down menus (do not exceed the maximum and minimum values listed). On BL12-2, a smaller size microbeam can also be selected.
  • The Show resolution button will open the resolution predictor to help choose the correct detector to sample distance
  • The Delete button will delete the current run definition, both parameters and helical path. To modify or delete a run after it has been started, use the button Reset.
  • To create a new helical collection definition, mount a new crystal, click on the * symbol below the current run number, and repeat the above process. If you want to recollect the data for the current crystal, use the Copy button. This will copy both the current data collection parameters and helical path definition to the next run. The check button Only Show Current Crystal will only display the helical definition for the currently selected run, and hide the others. By default, when clicking on different runs, the sample will be translated so that the beam is centered on the helical path defined for that run; checking the Hold Sample Position While Viewing Other Crystals will prevent the sample translation motors from moving -however, phi will still rotate to the value where the last point of the helical path was saved.

Using Webice in conjunction with the Helical Tab

Webice can be used to calculate delta phi and the start end end angles, and also the exposure time/attenuation per image (provided that you use the same beam size selected in the Helical data collect setup). However, the Webice run cannot be exported to the Helical tab yet, so the relevant values determined by the strategy must be entered by hand.

Note that the total dose calculated by Web-Ice for the suggested phi range assumes that the data will be collected at a single position and will be therefore an overestimation of the dose in the helical data collection. A better estimate of the dose can be obtained by multiplying the total Webice dose by the beam size along the helical path and dividing it by the crystal length. For example, if you collect a total of 90 degrees from a crystal 0.5 mm long with a beam size of 50 microns and the predicted dose for 90 degrees is 10MGy, the estimated maximum dose during the helical data collection will be 10 x 0.05 / 0.5 = 1 MGy. It is recommended that no portion of the crystal recieves a dose superior to 10-30 MGy, or for crystals at room temperature, 0.1-0.3 MGy.

Web-Ice can also be used multicrystal strategy option in Web-Ice to optimize the starting phi angle for successive crystals whenever it is not possible to collect all the data from a single sample.

MAD and SAD data collection

MAD data collection in wedges is not supported in the Helical Tab: each image collected at a different position along the crystal is defined as a wedge, and it takes a prohibitive amount of time to change energy for each image. However, SAD data collection in inverse beam can be selected by clicking on the Inverse beam button. This will collect a second image at 180 degrees before translating the crystal to the next position.

MAD data collection from a single crystal can be done by using the Copy button mentioned above to clone the run, and repeat the same helical pass at a different energy. To mitigate radiation damage, the best practice is to collect a relatively small angle per helical run (the value for the "wedge" calculated by Web-Ice is a good suggestion) Once the same angle range has been collected at two or more energies, the runs can be copied again, this time increasing the starting phi and image number.

Monitoring the Data Collection

The Collect Frame View widget shows the details of the frames that will be collected during the helical data collection. It shows the frame name, position information, starting phi value for that frame, wavelength, file prefix, frame number, and the total number of frames left to collect in that position.

The diffraction images are displayed in the Diffraction Image View widget, with the same functionality as on other Blu-Ice tabs.