BeamTilt vs IS CryoARM300

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Name	BeamTilt vs IS CryoARM300
Permalink	https://serialemscripts.nexperion.net/script/71
Category	Calibrations
Language	SerialEM Scripting
Description	The goal is to measure BT and STIG vs IS after shifting beam in different directions
Author	Marcus Fislage
Literature reference	https://journals.iucr.org/m/issues/2020/04/00/pw5013/index.html
Website link	http://www.becm.be

Version History

Version 1 (April 02, 2021; 354 download(s); SerialEM version ≥ 3.8)

Version 1

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Upload date	April 02, 2021
Download count	354
SerialEM version ≥	3.8

ScriptName BTvsIS

###################################
#
# Script to acquire SPA data
#
# R. Efremov & M.Fislage Jan 2021
#
# Script modified version of https://sphinx-emdocs.readthedocs.io/en/latest/serialEM-note-tackle-coma.html
#The goal is to measure BT and STIG vs IS after shifting beam in different directions
#
# Use ReportComaVsISmatrix 
#
# to check actual values of xpx xpy ypx ypy
#
# Use DebugOutput 1 to get details of the image shift
#   
# STATUS: functional
#
###################################

# BTx = ISx * xpx + ISy * xpy

# BTy = ISx * ypx + ISy * ypy

SetImageShift 0 0

SetProperty AstigBTBacklashDelay 2
IS_ScailFact = 3.25 # Rough scaling factor

extent = { 8.0  } # SHIFTS IN MICRONS (approximate)

echo *********************************************************************************************************************
echo STARTING SCRIPT BTvsIS 
echo *********************************************************************************************************************
echo RUN COMA and ASTIGMATISM MEASUREMENTS FOR IS $extent
echo DO STIG AND COMA CORRECTION AT IS 0

#Initial alignment at  IS = 0 
FixAstigmatismByCTF
FixComaByCTF
FixAstigmatismByCTF

# main program

ReportImageShift xbase ybase
ReportBeamTilt    txbase tybase
Loop $#extent ind
   echo ************************MEASURING TILTS FOR IS  $extent[$ind] microns*************************
   
   SetImageShift  ( $xbase + $extent[$ind] * $IS_ScailFact  )  $ybase
   ScreenDown
   Delay 20 sec
   ScreenUp
   Delay 2 sec
   FixComaByCTF 1 1 0   
   ReportComaTiltNeeded xpxplus ypxplus
   SetBeamTilt ( $txbase + $xpxplus ) ( $tybase + $ypxplus )
   FixAstigmatismByCTF 1 1
   ReportStigmatorNeeded  xsxplus ysxplus    
   SetBeamTilt $txbase $tybase
   echo  IS X plus BEAM TILT IS $xpxplus $ypxplus mrad and STIG  $xsxplus $ysxplus units
   
   SetImageShift ( $xbase - $extent[$ind] * $IS_ScailFact )  $ybase
   ScreenDown
   Delay 20 sec
   Delay 2 sec
   ScreenUp
   FixComaByCTF 1 1 0
   ReportComaTiltNeeded xpxminus ypxminus
   SetBeamTilt ( $txbase + $xpxminus ) ( $tybase + $ypxminus )
   FixAstigmatismByCTF 1 1
   ReportStigmatorNeeded  xsxminus ysxminus    
   SetBeamTilt $txbase $tybase
   echo  IS X minus BEAM TILT IS $xpxminus $ypxminus mrad and STIG  $xsxminus $ysxminus units
   
   SetImageShift $xbase  ( $ybase + $extent[$ind] * $IS_ScailFact  )
   ScreenDown
   Delay 20 sec
   ScreenUp
   Delay 2 sec
   FixComaByCTF 1 1 0
   ReportComaTiltNeeded xpyplus ypyplus
   SetBeamTilt ( $txbase + $xpyplus ) ( $tybase + $ypyplus )
   FixAstigmatismByCTF 1 1
   ReportStigmatorNeeded  xsyplus ysyplus    
   SetBeamTilt $txbase $tybase
   echo  IS Y plus BEAM TILT IS $xpyplus $ypyplus mrad and STIG  $xsyplus $ysyplus units
   
   
   SetImageShift $xbase  ( $ybase - $extent[$ind] * $IS_ScailFact )
   ScreenDown
   Delay 20 sec
   ScreenUp
   Delay 2 sec
   FixComaByCTF 1 1 0
   ReportComaTiltNeeded xpyminus ypyminus
   SetBeamTilt ( $txbase + $xpyminus ) ( $tybase + $ypyminus )
   FixAstigmatismByCTF 1 1
   ReportStigmatorNeeded  xsyminus ysyminus    
   SetBeamTilt $txbase $tybase
   echo  IS Y minus BEAM TILT IS $xpyminus $ypyminus mrad and STIG  $xsyminus $ysyminus units
   
   
   SetImageShift $xbase  $ybase
   
   
   xpx = ($xpxplus - $xpxminus) / (2 * $extent[$ind] * $IS_ScailFact )
   xpy = ($xpyplus - $xpyminus) / (2 * $extent[$ind] * $IS_ScailFact )
   ypx = ($ypxplus - $ypxminus) / (2 * $extent[$ind] * $IS_ScailFact )   
   ypy = ($ypyplus - $ypyminus) / (2 * $extent[$ind] * $IS_ScailFact )
   
   echo ********************** MATRISES for extent $extent[$ind]   **********************
   echo   BTvs IS matrix = $xpx $xpy  $ypx $ypy
   
   xsx = ($xsxplus - $xsxminus) / (2 * $extent[$ind] * $IS_ScailFact )
   xsy = ($xsyplus - $xsyminus) / (2 * $extent[$ind] * $IS_ScailFact )
   ysx = ($ysxplus - $ysxminus) / (2 * $extent[$ind] * $IS_ScailFact )   
   ysy = ($ysyplus - $ysyminus) / (2 * $extent[$ind] * $IS_ScailFact )
   
   echo  STIG vs IS matrix = $xsx $xsy $ysx $ysy
   
EndLoop
SetProperty AstigBTBacklashDelay 0
echo *********************************************************************************************************************
echo END SCRIPT BTvsIS 
echo *********************************************************************************************************************
EndMacro

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/)