Parameters Script JEOL CryoARM

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Name	Parameters Script JEOL CryoARM
Permalink	https://serialemscripts.nexperion.net/script/59
Category	Single Particle
Language	SerialEM Scripting
Description	Parameters Script to modify input parameters for SPA data collection on JEOL CryoARM
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 2

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Upload date	April 02, 2021
Download count	264
SerialEM version ≥	3.8

MacroName Parameters
##################################
#
# Script to include all the parameters used in all the scripts
# It should be called in the beginning of any main script.
# It should be used with the new versions of Function script and SPA and allows for fast multiple collection
# Vector 1 and Vector 2 can be obtained by running the new script hole pattern
# ComaIS and ComaStig matrices, used for coma and stig correction of multiple can be obtained within SerialEM through the ComavsIS calibration
#
# M.Fislage & R. Efremov Jan 2021
# Credits to J. Brink, Chen Xu and David Mastronarde
#
# STATUS: functional
#
###################################

# Define focus parameters in microns

TD_low = -0.8		# defocus limit low
TD_high = -1.6		# defocus limit high
step = 0.2                                    # defocus step interval	
FocusDistance = 1   	# distance between acquisition positions used for physical focusing in microns

# Define multi shot parameters used in SPA

shots = 5  	# no of shots around the center
center = 0		#-1 first shot in center, 1 last shot in center, 0 no center shot (not available for shottype=0)
offset = 0.67		# offset from center in microns
msdelay = 0 		# extra delay between multishot images in seconds

wait_time = 0   # delay in sec before each new image is recorded

#hole pattern parameters

#single hole
#hole_coord_x = { 0 }
#hole_coord_y = { 0 }

# 2x2 pattern with 0.0 in the middle in between all the holes
hole_coord_x = { -0.5 0.5 0.5 -0.5 }
hole_coord_y = { -0.5 -0.5 0.5 0.5 }

# 3x1 pattern with 0.0 in the middle in between all the holes
#hole_coord_x = { -1 0 1 }
#hole_coord_y = { 0 0 0 }

# 2x2 + 1 pattern with 0.0 in the middle
#hole_coord_x = { 0 1 0 0 -1 }
#hole_coord_y = { -1 0 0 1 0  }

# 3x3 pattern with 0.0 in the middle
#hole_coord_x = { -1 0 1 -1 0 1 -1 0 1 }
#hole_coord_y = { 1 1 1 0 0 0 -1 -1 -1 }

# 5x5 pattern with 0.0 in the middle
#hole_coord_x = { -2 -2 -2 -2 -2 -1 -1 -1 -1 -1 0 0 0 0 1 1 1 1 1 2 2 2 2 2 0 }
#hole_coord_y = { -2 -1 0 1 2 -2 -1 0 1 2 -2 -1 1 2 -2 -1 0 1 2 -2 -1 0 1 2 0 }

#G VECTORS ID2800
VECTOR1 = {4.248573  8.643833}
VECTOR2 = {-9.88568  3.596413}

ComaISmatrix = {-0.068739  0.060608  -0.056379  -0.078368 }
ComaSTIGmatrix = {0.000729  -0.000301  -0.001173  -0.001173}

# Frequency of beam focusing in minutes

BeamCentTimeInterval = 1  # Frequency of Beam Centering in minutes

# Ice thickness frequency

I_EMPTY = 950		# beam count of empty area
ICE_FREQ = 10		# frequency of ice measurement with filter slit (counted in holes)

# Interval in hours for flashing the CFEG
FlashInterval = 4.5

# Interval to prepare HW Dark Reference
DarkRefInterval = 3

# Additonal delay for stage stabilization before image acquisition

STAGE_STAB_TIME = 5

# send emails for low intensity images

IntensityThreshold = 15      	# threshold for image to be considered low Intensity
NoLowCountImages = 5    	# No of low intensity images +1 that will trigger a warning email
debug_tur = 0                                # 1 - output additonal information, 0 - no output

#DO NOT TOUCH THESE VALUES
IS_shift_x_micron = {3.252 -1.332 }
IS_shift_y_micron = {-1.425 -2.693}
EndMacro

Documentation

Parameters in this script will be called by the SPA script for JEOL CryoARM300
Changes in Version 2:
It should be used with the new versions of Function script and SPA and allows for fast multiple collection
Vector 1 and Vector 2 can be obtained by running the new script hole pattern
ComaIS and ComaStig matrices, used for coma and stig correction of multiple can be obtained within SerialEM through the ComavsIS calibration
Select the correct hole pattern to decide which multihole scheme you would like to use

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/)