# command file to run ctfplotter
#
####CreatedVersion#### 3.12.20
# 
#
$${IMOD_DIR}/ctfplotter/ctfplotter -Stand
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InputStack  MTEg5series6D.st
#
# The tilt angle file - .rawtlt could be used instead if .tlt not available yet
AngleFile   MTEg5series6D.tlt
DefocusFile MTEg5series6D.defocus
#
# How many degrees the tilt axis deviates from vertical (Y axis) (CCW positive)
AxisAngle	-3.3
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# Image pixel size in nanometers
PixelSize	0.53
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# Expected defocus at the tilt axis in nanometers (underfocus is positive)
ExpectedDefocus	6000.0
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# Starting and ending tilt angles for initial analysis
AngleRange  -20.0  20.0
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# Microscope voltage in kV
Voltage	200
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# Microscope spherical aberration in millimeters
SphericalAberration	2.0
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# Fraction of amplitude contrast
AmplitudeContrast	0.07
#
# Defocus tolerance in nanometers defining the center strips
DefocusTol   200
PSResolution 101
TileSize     256
LeftDefTol  2000.0
RightDefTol 2000.0 
ConfigFile	/usr/local/ImodCalib/CTFnoise/DE-12Test/DE-12Div2.cfg
$if (-e ./savework) ./savework