SerialEM Note: Setup LD with Mix of µP and nP Modes

Author

Chen Xu

Contact

<chen.xu@umassmed.edu>

Date-created

2018-03-31

Last-updated

2020-09-21

Abstract

There are cases and situations that people want to use nanoprobe(nP) mode , but nP is not comfortable for lower mag range such as first a few magnifications just above LM, because the beam doesn’t spread wide enough to cover entire camera area. This forces us to use µP for View and nP for rest of LD areas, namely F, T and R etc..

However, most people find it hard to setup LD conditions with the mix of nP and µP modes. I had frustrated time doing so too. This is, I think, mainly because nP and µP don’t share the same origins for beam shift and defocus (and beam tilt too) - they have their one origins. In SerialEM, all the LD conditions are linked together. Therefore, the seprate origins of focus and beam shift for µP and nP modes give extra hard time setting up LD in this mix use of nP and µP.

SerialEM already has a way to deal with this problem. I hope this doc makes it clearer and easier to follow practically.

Procedure Setting Up LD with µP and nP

In my case, I use µP for View area with -300 microns focus offset. All other areas - F, T and R are with nP. I usually use the same spot size for everything.

  1. Before LD is turned on, make sure beam is centered for both µP and nP beam. I usually use Direct Alignments to do this with µP and nP beam. That is, turn µP on, Directly Alignments - Beam Shift (multi-function to center) - done. Repeat with nP mode.

  2. Turn on SerialEM LD.

  3. Lower Down large screen or insert screen.

  4. From Task - Specialized Options, make sure the “Adjust Focus on Probe Mode Change” is NOT checked.

  5. Set View Defocus Offset to 0 using dial Up-Down button on SerialEM LD Control Panel.

  6. Select R area (radio button) on LD control panel.

  7. On microscope right panel, press “Eucentric Focus”.

  8. Reset Defocus (L2 button on our current setup for soft buttons, yours could be different), this makes defocus display 0.

  9. Select V area (radio button) on LD control panel.

  10. wait 6-7 seconds to allow scope to switch to this mag and µP mode.

  11. On microscope right panel, press “Eucentric Focus”.

  12. Reset Defocus (L2 button on our current setup for soft buttons, yours could be different), this makes defocus display 0.

  13. Set View Defocus Offset to target value (e.g., -300) using dial Up-Down button on SerialEM LD Control Panel.

  14. From Task - Specialized Options, make sure the “Adjust Focus on Probe Mode Change” is NOW checked.

That’s it.