TuneScope

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Details

Name	TuneScope
Permalink	https://serialemscripts.nexperion.net/script/47
Category	Calibrations
Language	SerialEM Scripting
Description	Script to tune Polara, Talos Arctica and/or Titan Krios
Author	Wim Hagen

Version History

Version 0.1 (April 08, 2019; 453 download(s); SerialEM version ≥ 3.7)

Version 0.1

Download

Upload date	April 08, 2019
Download count	453
SerialEM version ≥	3.7

MacroName TuneScope

# 20190408 Wim Hagen, EMBL Heidelberg
# Script to tune the Krios
# Focus is set to zero
# Loop focus measurement and set stage height to get the desired defocus
# Run Zemlin tableau, iterate when out of spec.
# Dialog asking to insert and center objective aperture
# AutoStigmate with objective aperture

# Setup low dose.
# Switch low dose off.
# If needed drop the spot size one or two steps, DO NOT CHANGE BEAM SIZE!!! 
# Burn a carbon area clean to get nice Thon-rings.
# Adjust desired defocus.
# start script and sit back.

###################################################

defocusoffset = -2  # defocus target in micrometers to be used for tuning, -2.5 for high mag, -6 to -8 for lower mags

###################################################

# binning 2
SetUserSetting CtfBinning 2 1

# 2 sec exposure
SetUserSetting CtfExposure 2 1

# full field of view
SetUserSetting CtfUseFullField 1 1

# no full array
SetUserSetting CtfDoFullArray 0 1

# Show life FFT
SetUserSetting SideBySideFFT 1 1

# set microcope focus to zero
SetDefocus 0

# focus with stage Z
Loop 2
   G -1
   ReportAutofocus 
   t  =  -1 * $RepVal1 + $defocusoffset
   if $t >= 0
      changeZ = $t + 3
      MoveStage 0 0 $changeZ
      MoveStage 0 0 -3
    elseif $t <= 0
      MoveStage 0 0 $t
   endif
   echo --> Z moved $t micron 
EndLoop

# auto-stigmate
FixAstigmatismByCTF 0 1

# Zemlin tableau
FixComaByCTF 0 1 0

# insert and center objective aperture
Pause  Insert and center objective aperture. Be sure to go out of diffraction mode before continuing!

# auto-stigmate
FixAstigmatismByCTF 0 1

SetUserSetting SideBySideFFT 0

Documentation

Setup low dose.
Switch low dose off.
If needed drop the spot size one or two steps, DO NOT CHANGE BEAM SIZE!!!
Burn a carbon area clean to get nice Thon-rings.
Adjust desired defocus.
Start script and sit back.

The script:
Focus is set to zero
Loop focus measurement and set stage height to get the desired defocus
Run Zemlin tableau, iterate when out of spec.
Dialog asking to insert and center objective aperture
Autostigmate with objective aperture

License

This code can be shared and adapted under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (https://creativecommons.org/licenses/by-nc-sa/4.0/)