Parameters

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Details

Name	Parameters
Permalink	https://serialemscripts.nexperion.net/script/16
Category	Single Particle
Language	SerialEM Scripting
Description	macro to include all the parameters used in all the macros It should be called in the beginning of any main macro
Author	Henning Stahlberg
Literature reference	http://www.bio.brandeis.edu/KeckWeb/emdoc/en_US.ISO8859-1/articles/SerialEM-howto:macro-explain/x248.html
Website link	http://c-cina.org

Version History

Version 1.0 (February 24, 2017; 548 download(s); SerialEM version ≥ (untested))

Version 1.0

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Upload date	February 24, 2017
Download count	548
SerialEM version ≥	(untested)

###################################################################
# macro to include all the parameters used in all the macros
# It should be called in the beginning of any main macro
###################################################################
#
# Daniel Caujolle-Bert, Henning Stahlberg, C-CINA, Biozentrum, University of Basel
# Feb. 25, 2017
#
MacroName Parameters

# Echo ---> Calling Parameters ...

## Defin the type of grid: 1=Quantifoil, 2=Lacey
GridType = 1

## for CycleTargetDefocus (um), default step is 0.1(um)
TD_low = -1.4
TD_high = -2.5

## for Drift 
# skip = 1 -> no drift control
# skip = 0 -> drift control
# drift rate threshold (A/sec.), only get used for skip = 0
skip = 0
crit = 1.5

# this is for no return for Record Frame exposure for a K2 camera.      
noReturn = 40

# Define, if you want to see the recorded image for every movie (DisplayOnly=1) or 
# only for every 10th movie (DisplayOnly=10) or even more rarely:
DisplayOnly = 1

# Define, how often the microscope should focus: 
# focusEachHole := 0   means to keep focus target constant and focus always.
# focusEachHole := 1   means to increment focus target and focus always.
# focusEachHole := 5   means to increment focus target and focus only every 5th image.
focusEachHole := 1

# Number of shots in one hole is $NumberShots
# Radius of off-center ImageShift displacement is $IS_RAD
NumberShots := 1
IS_RAD := 0.7

Related Scripts

The following scripts provide a similar or related functionality, but are not required to run this script:

Documentation

Based on a concept by Chen Xu,
http://www.bio.brandeis.edu/KeckWeb/emdoc/en_US.ISO8859-1/articles/SerialEM-howto:macro-explain/x248.html

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/)