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Hutch Tab

The Hutch Tab allows the users to adjust various parameters for data collection by entering the desired values into the input boxes found in the Hutch Overview menu. If changes cannot be made, the input box is greyed out or inactive, hovering the mouse over the input box will return an error message. The changes are shown in red and are not made until the Start button is pressed. Hitting the Cancel button restores the edited motor values to their current position. Once the Start button is pressed, and the changes are initiated, the parameter being changed will be highlighted in red. Hitting the Abort button will stop the changes while they are being made. In general, all motors will remain at the position at which the Abort button was pressed.

Pull-Down Menus

  • The pull-down menus next to input boxes show the minimum and maximum values for the particular control with a range of values in between.
  • Any values can be input within this range. Entering values outside the range is strongly discouraged - you may get an error message , or hit a motor hardware limit, which will result in miscalibration of the motor.
  • Clicking on the units will produce another drop down menu with alternative units.
  • Clicking on the name of the parameter will produce a window presenting the option to undo the last change of that parameter.

Min. and max. values

Alternative units

Undo

  • If your experiment requires data collection outside the range provided, contact your support staff.

Mounting the Crystal
  • General directions for mounting a crystal in a cryoloop can be found in this slide show.
  • Move the detector and beamstop away from the sample for easy mounting. Please do not attempt to adjust the beam stop manually. If the beamstop is bent out of the beam or broken it will expose the detector to direct beam and damage it.
  • Practice mounting a pin with a blank loop on the goniometer to make sure your system is compatible with our coaxial cold stream. Contact Staff if you run in to any problems.
  • Check that the cold stream is aligned correctly (nozzle to sample distance should be ~10mm).
  • Mount your sample on the goniometer head.
  • Move the beamstop back into place.
  • Use the resolution predictor to calculate the optimal beamstop distance.
  • If you will be using the Stanford Automated Mounting (SAM) robot for mounting your crystals, see either the Sample tab or the Screening tab for further instructions.

Crystal Centering

  1. Select the Sample tab on the video display.
  2. Select the zoom level Low to find the sample.
  3. Click on the sample to center it.
  4. Rotate phi 90 degrees.
  5. Click on the sample once again to center.
  6. Select zoom level high.
  7. Repeat steps 2 to 4 to align the crystal accurately.

If you want to hit the crystal in a very precise spot and you cannot click on it accurately enough with the mouse you can use the "Move Sample" buttons. The double arrow buttons translate the sample horizontally by half a screen. The single arrow buttons translate the sample vertically or horizontally by one pixel.


Auto Centering

  • The sample can be quickly aligned by selecting Center Loop.
  • This automated procedure sometimes fails if the lighting or sample shape is abnormal.
  • If the sample is asymmetric in the loop, a manual adjustment at zoom level High may be required.


Sample Lighting

To address the needs of remote users, an improved sample visualization system has been developed that provides remote control of the light intensity and direction. With this new system, during automated loop centering the lighting is automatically changed to the optimal settings for this process. Once loop centering is complete, the lighting is returned to configurable default settings. These settings may be adjusted using controls displayed in the Blu-ice GUI below.

    back lighting

    side lighting

    both lights on

This sample illumination system consists of two light sources:

  • Back lighting: a uniform back light, developed in house and composed of an array of 81 ultra-bright LEDs. This light typically shows as a blue background. With this lighting only, the loop is normally seen as a dark sillouette, as shown above in the first image. This is optimal for automated loop centering using the Center Loop button, or with automated loop centering used in conjunction with automated sample screening (see the Screening tab for further instructions). This light can either be switched on or off using the Back Light button.
  • Side lighting: a variable intensity side light comprised of an optical fiber bundle connected to a Schott Fostec model DCRIII halogen source. This source is directed at the crystal from an angle of 45 degrees, mounted above the X-ray beam. With this lighting, the background is generally dark and the loop and crystal are seen clearly, as shown in the second image above. The intensity of this lighting can be adjusted using the Side Light Intensity slidebar as shown below.
  • The two lights can be used in conjunction, and the intensity of the side light adjusted accordingly to provide optimum visualization of the crystal, as shown in the third image above.

Sample Orientation

The Omega and Kappa motors are currently locked to avoid collisions with the detector and other beamline hardware.


If Omega or Kappa values need to be changed, please contact your support staff.


Adjusting Beam Attenuation


  • When the detector is saturated, or has too many overloads, the beam needs to be attenuated to ensure accurate data collection. Attenuating the beam can also account for exposure times shorter than the rotation time of phi. Aluminum filters are used to attenuate the beam.
  • High energy beams cannot be fully attenuated by the aluminum filters. Raising the energy of the beams will lower the attenuation.
  • Filters already in place can be seen on video through the panel tab. On the drop down menu choose the Filter Controller view.
Critical: Note that it is possible to set the attenuation for each data collection run. The value entered for the data collection run will override the value entered in the hutch tab.

Adjusting Beam Size and Energy

Beam Size

  • To adjust the beam size click on the windows labeled Width and Height under the beam size label (see the first image above). The white box on the Hutch monitor gets updated automatically to the input value. Like all other Blu-ice paramters, the color of this box becomes red if the current value is not same as the value in the input box. The beam should be optimized after changing the beam size using the Optimize Beam button located under the energy display.
  • Clicking on the units will open a drop down menu that allows the units to be changed.
  • Ideally the beam size should be the same as the crystal size. However, due to horizontal crossfire, beam sizes of less than 100 micron width will reduce the beam intensity.

Energy

  • To change the energy use the box labeled Energy.
  • When first started, Blu-Ice shows the energy in eV. The energy units can be changed to keV and A by clicking on the current unit as seen in the second image above. Click Start to initiate any changes that you make.
  • The input value must be the same as the selected unit. Entering a value of a different unit will result in an error.
  • The beamline control software uses a new scripted device "optimized energy" which automatically optimizes the energy if it changes by more than 500eV (including during MAD experiments) and also every 1/2 - 2 hours depending on the beamline.

Adjusting Detector Position

  • To adjust the detector distance, vertical or horizontal position, change the values in the corresponding box. You will notice in the Resolution Predictor below the Detector Position control that the beam center and the predicted resolution circles move. See Determining Resolution Limits for more details.
  • Pressing Start will move the detector to the set position.
  • To view the detector position on video, go to the Hutch Tab in the video section and select overview from the presets on the left.

Determining Resolution Limits

  • The high and low resolution limit at a particular detector and beamstop position may be determined using the box labeled Resolution Predictor. When a change in the detector position, beamstop position or energy is made, the view in this box is updated automatically.
  • The label on the largest circle that fits in the detector shows the resolution to which complete data can be collected. Partial circles limit resolution shells that will be incomplete.
  • The label on the smallest circle corresponds to the lowest resolution to which data will be collected.
  • The Vertical and Horizontal positions of the detector (see Adjusting Detector Position section above) can also be used to determine the amount of detector offset you may require. Any movement of these positions will also be updated automatically on the Resolution Predictor.
  • If you do not wish to offset the detector, remember to reset the Horizontal and Vertical positions to the desired values before starting the data collection.