Coma vs. Image Shift Calibration Dialog

This dialog box allows you to calibrate how beam tilt must be changed to achieve coma-free alignment when an image shift is imposed.  It has entries for the maximum image shift to be tested and a rotation angle for the image shift vectors to apply.  The calibration involves running the Coma-free Alignment by CTF routine to measure the beam tilt needed at four locations. At each position, the measured beam tilt is applied temporarily and astigmatism is measured so that its dependence on image shift is also calibrated.  The calibration can then be applied by the multi-shot routine (see Set Multi-Shot Parameters) and with several script commands. When this dialog is open in Low Dose mode, the areas that will be tested are drawn on a View or Search image.  With a rotation of 0, image shift will be changed in +/-X then in +/-Y by the amount corresponding to the shift in microns entered in the Distance to measure in each direction text box.  When a non-zero value is set in the Rotation of measurement vectors text box, these basic vectors are rotated by that amount.  With these features, you can avoid running the coma-free alignment over a hole.

The choices for Measure coma with are 1) use just 5 positions, as was the case prior to SerialEM 4.1; 2) use a full array of 9 positions, which will take longer but may be more accurate; or 3) use whatever has been chosen for running the routine to fix coma.

It is important to realize that this calibration strictly applies only under the current illumination conditions (specifically, the C2/C3 lens setting or illuminated area, and the probe mode or alpha setting).  When near parallel illumination, it may not change much with beam changes; otherwise it might change considerably.  This has several consequences:

• It may be necessary to do the calibration once per session, after setting up the illumination to be used for acquisition.
• The calibration should be done in Low Dose mode if acquisition is to be done in Low Dose mode
• Because it depends on your settings for illumination, the calibration will be saved in your settings file, not shared with others using other settings files.
• The calibration can be checked with the the Test Multishot Positions button in the Multiple Record Setup dialog and with the script command 'TestNextMultiShot 2' (see Testing Image Location and Coma Adjustment) ,or with a script like
     FixComaByCTF
     ImageShiftByMicrons 2 0 1 1
     Delay 3
     FixComaByCTF 1 1
     FixAstigmatismByCTF 1 1
  where you could omit the first FixComaByCTF if you have already done the coma-free alignment, the "2 0" can be replaced by an image shift of your choice, the astigmatism test could be omitted, and you could add additional tests at other image shift positions.  Such a script could be used to explore how much the adjusted beam tilt gets off when the beam intensity is changed.