# Amira Project 202320
# Amira3D
# Generated by Amira3D 2023.2-beta-1
remove -all
remove "grayScaleInverted.am" "physics.icol" "grayScale.am" "tomogram_subvol.am" "3j9i-pdb.amf" "proteasome8.pointcloud.am" "Ortho Slice" "Molecule Cloud View" "Bounding Box" "Bounding Box 2"

# Create viewers
viewer setVertical 0

viewer 0 setTransparencyType 6
viewer 0 setAutoRedraw 0
viewer 0 show
mainWindow show

_units setUnitsManagementMode 0

set hideNewModules 1
[ load ${AMIRA_ROOT}/data/colormaps/grayScaleInverted.am ] setLabel "grayScaleInverted.am"
"grayScaleInverted.am" setIconPosition 0 0
"grayScaleInverted.am" setNoRemoveAll 1
"grayScaleInverted.am" setVar "CustomHelp" {HxColormap256}
"grayScaleInverted.am" fire
"grayScaleInverted.am" setMinMax 0 255
"grayScaleInverted.am" flags setValue 1
"grayScaleInverted.am" shift setMinMax -1 1
"grayScaleInverted.am" shift setButtons 0
"grayScaleInverted.am" shift setEditButton 1
"grayScaleInverted.am" shift setIncrement 0.133333
"grayScaleInverted.am" shift setValue 0
"grayScaleInverted.am" shift setSubMinMax -1 1
"grayScaleInverted.am" scale setMinMax 0 1
"grayScaleInverted.am" scale setButtons 0
"grayScaleInverted.am" scale setEditButton 1
"grayScaleInverted.am" scale setIncrement 0.1
"grayScaleInverted.am" scale setValue 1
"grayScaleInverted.am" scale setSubMinMax 0 1
"grayScaleInverted.am" fire
"grayScaleInverted.am" setViewerMask 16383

set hideNewModules 1
[ load ${AMIRA_ROOT}/data/colormaps/physics.icol ] setLabel "physics.icol"
"physics.icol" setIconPosition 0 0
"physics.icol" setNoRemoveAll 1
"physics.icol" fire
"physics.icol" setMinMax 0 1
"physics.icol" flags setValue 1
"physics.icol" shift setMinMax -1 1
"physics.icol" shift setButtons 0
"physics.icol" shift setEditButton 1
"physics.icol" shift setIncrement 0.133333
"physics.icol" shift setValue 0
"physics.icol" shift setSubMinMax -1 1
"physics.icol" scale setMinMax 0 1
"physics.icol" scale setButtons 0
"physics.icol" scale setEditButton 1
"physics.icol" scale setIncrement 0.1
"physics.icol" scale setValue 1
"physics.icol" scale setSubMinMax 0 1
"physics.icol" fire
"physics.icol" setViewerMask 16383

set hideNewModules 1
[ load ${AMIRA_ROOT}/data/colormaps/grayScale.am ] setLabel "grayScale.am"
"grayScale.am" setIconPosition 0 0
"grayScale.am" setNoRemoveAll 1
"grayScale.am" setVar "CustomHelp" {HxColormap256}
"grayScale.am" fire
"grayScale.am" setMinMax 0 255
"grayScale.am" flags setValue 1
"grayScale.am" shift setMinMax -1 1
"grayScale.am" shift setButtons 0
"grayScale.am" shift setEditButton 1
"grayScale.am" shift setIncrement 0.133333
"grayScale.am" shift setValue 0
"grayScale.am" shift setSubMinMax -1 1
"grayScale.am" scale setMinMax 0 1
"grayScale.am" scale setButtons 0
"grayScale.am" scale setEditButton 1
"grayScale.am" scale setIncrement 0.1
"grayScale.am" scale setValue 1
"grayScale.am" scale setSubMinMax 0 1
"grayScale.am" fire
"grayScale.am" setViewerMask 16383

set hideNewModules 0
[ load ${SCRIPTDIR}/data/tomogram_subvol.am ] setLabel "tomogram_subvol.am"
"tomogram_subvol.am" setIconPosition 20 10
"tomogram_subvol.am" setVar "CustomXML" {tomogram_subvol.am_config.xml}
"tomogram_subvol.am" sharedColormap disconnect
"tomogram_subvol.am" sharedColormap setDefaultColor 0.8 0.8 0.8
"tomogram_subvol.am" sharedColormap setDefaultAlpha 0.500000
"tomogram_subvol.am" sharedColormap activateLocalRange 1
"tomogram_subvol.am" sharedColormap setLocalMinMax 0.000000 1.000000
"tomogram_subvol.am" sharedColormap enableAlpha 1
"tomogram_subvol.am" sharedColormap enableAlphaToggle 1
"tomogram_subvol.am" sharedColormap setAutoAdjustRangeMode 1
"tomogram_subvol.am" fire
"tomogram_subvol.am" setViewerMask 8191

set hideNewModules 0
[ load -amf ${SCRIPTDIR}/data/3j9i-pdb.amf ] setLabel "3j9i-pdb.amf"
"3j9i-pdb.amf" setIconPosition 20 45
"3j9i-pdb.amf" setVar "CustomXML" {3j9i-pdb.amf_config.xml}
"3j9i-pdb.amf" fire
"3j9i-pdb.amf" time setMinMax 0 1
"3j9i-pdb.amf" time setSubMinMax 0 1
"3j9i-pdb.amf" time setValue 0
"3j9i-pdb.amf" time setDiscrete 1
"3j9i-pdb.amf" time setIncrement 1
"3j9i-pdb.amf" time animationMode -once
"3j9i-pdb.amf" time setAnimationDelay 10
"3j9i-pdb.amf" transformation setIndex 0 0
"3j9i-pdb.amf" selection setOptValue 0 0
"3j9i-pdb.amf" fire
"3j9i-pdb.amf" fire
"3j9i-pdb.amf" setViewerMask 8191

set hideNewModules 0
[ load ${SCRIPTDIR}/data/proteasome8.pointcloud.am ] setLabel "proteasome8.pointcloud.am"
"proteasome8.pointcloud.am" setIconPosition 20 80
"proteasome8.pointcloud.am" setVar "CustomHelp" {HxCluster}
"proteasome8.pointcloud.am" setVar "CustomXML" {HxCluster_config.xml}
"proteasome8.pointcloud.am" fire
"proteasome8.pointcloud.am" setViewerMask 8191

set hideNewModules 0
create HxOrthoSlice "Ortho Slice"
"Ortho Slice" setIconPosition 367 10
"Ortho Slice" setVar "CustomHelp" {HxOrthoSlice}
"Ortho Slice" setVar "CustomXML" {HxOrthoSlice_config.xml}
"Ortho Slice" data connect "tomogram_subvol.am"
"Ortho Slice" fire
"Ortho Slice" sliceOrientation setValue 0
"Ortho Slice" fire
"Ortho Slice" origin  setBoundingBox -3.40282e+38 3.40282e+38 -3.40282e+38 3.40282e+38 -3.40282e+38 3.40282e+38
"Ortho Slice" origin  setImmediateMode 0
"Ortho Slice" origin  setOrtho 0
"Ortho Slice" origin  showDragger 0
"Ortho Slice" origin  showPoints 0
"Ortho Slice" origin  setPointScale 1
"Ortho Slice" origin  showOptionButton 1
"Ortho Slice" origin  setNumPoints 1 1 1
"Ortho Slice" origin  setCoord 0 2458.5 2990.9 -762.3
"Ortho Slice" normal  setBoundingBox -3.40282e+38 3.40282e+38 -3.40282e+38 3.40282e+38 -3.40282e+38 3.40282e+38
"Ortho Slice" normal  setImmediateMode 0
"Ortho Slice" normal  setOrtho 0
"Ortho Slice" normal  showDragger 0
"Ortho Slice" normal  showPoints 0
"Ortho Slice" normal  setPointScale 1
"Ortho Slice" normal  showOptionButton 1
"Ortho Slice" normal  setNumPoints 1 1 1
"Ortho Slice" normal  setCoord 0 0 0 1
"Ortho Slice" options setValue 0 1
"Ortho Slice" options setToggleVisible 0 1
"Ortho Slice" options setValue 1 0
"Ortho Slice" options setToggleVisible 1 1
"Ortho Slice" options setValue 2 0
"Ortho Slice" options setToggleVisible 2 1
"Ortho Slice" mappingType setIndex 0 0
"Ortho Slice" contrastLimit setMinMax 0 -16777216 16777216
"Ortho Slice" contrastLimit setValue 0 7
"Ortho Slice" colormap connect "grayScale.am"
"Ortho Slice" colormap setDefaultColor 1 0.8 0.5
"Ortho Slice" colormap setDefaultAlpha 1.000000
"Ortho Slice" colormap activateLocalRange 1
"Ortho Slice" colormap setLocalMinMax 145.429962 166.328506
"Ortho Slice" colormap enableAlpha 1
"Ortho Slice" colormap enableAlphaToggle 1
"Ortho Slice" colormap setAutoAdjustRangeMode 0
"Ortho Slice" sliceNumber setMinMax 0 173
"Ortho Slice" sliceNumber setButtons 1
"Ortho Slice" sliceNumber setEditButton 1
"Ortho Slice" sliceNumber setIncrement 1
"Ortho Slice" sliceNumber setValue 87
"Ortho Slice" sliceNumber setSubMinMax 0 173
"Ortho Slice" transparency setValue 0
"Ortho Slice" alpha setMinMax 0 -16777216 16777216
"Ortho Slice" alpha setValue 0 0
"Ortho Slice" alpha setMinMax 1 -16777216 16777216
"Ortho Slice" alpha setValue 1 255
"Ortho Slice" frameSettings setState {item 0 1 item 2 1 color 3 1 0.5 0 }
"Ortho Slice" embossingOnOff setValue 0
"Ortho Slice" depth setMinMax -60 60
"Ortho Slice" depth setButtons 0
"Ortho Slice" depth setEditButton 1
"Ortho Slice" depth setIncrement 8
"Ortho Slice" depth setValue 2
"Ortho Slice" depth setSubMinMax -60 60
"Ortho Slice" fire

"Ortho Slice" fire
"Ortho Slice" setViewerMask 8191
"Ortho Slice" setShadowStyle 3
"Ortho Slice" setPickable 1

set hideNewModules 0
create HxMolCloudView "Molecule Cloud View"
"Molecule Cloud View" setIconPosition 315 80
"Molecule Cloud View" setVar "CustomHelp" {HxMolCloudView}
"Molecule Cloud View" setVar "CustomXML" {HxMolCloudView_config.xml}
"Molecule Cloud View" data connect "proteasome8.pointcloud.am"
"Molecule Cloud View" molecule connect "3j9i-pdb.amf"
"Molecule Cloud View" continuousColormap disconnect
"Molecule Cloud View" continuousColormap setDefaultColor 1 1 0.7
"Molecule Cloud View" continuousColormap setDefaultAlpha 1.000000
"Molecule Cloud View" continuousColormap activateLocalRange 1
"Molecule Cloud View" continuousColormap setLocalMinMax 0.000000 0.000000
"Molecule Cloud View" continuousColormap enableAlpha 1
"Molecule Cloud View" continuousColormap enableAlphaToggle 1
"Molecule Cloud View" continuousColormap setAutoAdjustRangeMode 1
"Molecule Cloud View" continuousColormap setColorbarMinMax 0 120
"Molecule Cloud View" discreteColormap disconnect
"Molecule Cloud View" discreteColormap setDefaultColor 0.475 0.922 0.58
"Molecule Cloud View" discreteColormap setDefaultAlpha 1.000000
"Molecule Cloud View" discreteColormap activateLocalRange 1
"Molecule Cloud View" discreteColormap setLocalMinMax 1.000000 28.000000
"Molecule Cloud View" discreteColormap enableAlpha 1
"Molecule Cloud View" discreteColormap enableAlphaToggle 1
"Molecule Cloud View" discreteColormap setAutoAdjustRangeMode 1
"Molecule Cloud View" discreteColormap setColorbarMinMax 0 120
"Molecule Cloud View" fire
"Molecule Cloud View" colorScheme setOptValue 0 2
"Molecule Cloud View" colorScheme setOptValue 1 0
"Molecule Cloud View" adaptiveSmoothing setValue 1
"Molecule Cloud View" fire
"Molecule Cloud View" setViewerMask 8191
"Molecule Cloud View" setPickable 1

set hideNewModules 0
create HxBoundingBox "Bounding Box"
"Bounding Box" setIconPosition 349 45
"Bounding Box" setVar "CustomHelp" {HxBoundingBox}
"Bounding Box" setVar "CustomXML" {HxBoundingBox_config.xml}
"Bounding Box" data connect "tomogram_subvol.am"
"Bounding Box" fire
"Bounding Box" options setState {item 0 0 color 1 1 0.5 0 item 3 0 }
"Bounding Box" lineWidth setMinMax 1 10
"Bounding Box" lineWidth setButtons 1
"Bounding Box" lineWidth setEditButton 0
"Bounding Box" lineWidth setIncrement 1
"Bounding Box" lineWidth setValue 1
"Bounding Box" lineWidth setSubMinMax 1 10
"Bounding Box" font setState {name: "Arial Unicode MS" size: 12 buttonText: Select bold: 0 italic: 0 color: 0.8 0.8 0.8}
"Bounding Box" fire
"Bounding Box" setViewerMask 16383,8191
"Bounding Box" setPickable 1

set hideNewModules 0
create HxBoundingBox "Bounding Box 2"
"Bounding Box 2" setIconPosition 336 116
"Bounding Box 2" setVar "CustomHelp" {HxBoundingBox}
"Bounding Box 2" setVar "CustomXML" {HxBoundingBox_config.xml}
"Bounding Box 2" data connect "proteasome8.pointcloud.am"
"Bounding Box 2" fire
"Bounding Box 2" options setState {item 0 0 color 1 1 0.5 0 item 3 0 }
"Bounding Box 2" lineWidth setMinMax 1 10
"Bounding Box 2" lineWidth setButtons 1
"Bounding Box 2" lineWidth setEditButton 0
"Bounding Box 2" lineWidth setIncrement 1
"Bounding Box 2" lineWidth setValue 1
"Bounding Box 2" lineWidth setSubMinMax 1 10
"Bounding Box 2" font setState {name: "Arial Unicode MS" size: 12 buttonText: Select bold: 0 italic: 0 color: 0.8 0.8 0.8}
"Bounding Box 2" fire
"Bounding Box 2" setViewerMask 16383,8191
"Bounding Box 2" setPickable 1

set hideNewModules 0

viewer 0 setCameraOrientation 1 0 0 3.14159
viewer 0 setCameraPosition 2025.34 2021.02 -5907.69
viewer 0 setCameraFocalDistance 5155.62
viewer 0 setCameraNearDistance 4375.41
viewer 0 setCameraFarDistance 5937.38
viewer 0 setCameraType perspective
viewer 0 setCameraHeightAngle 44.7462
viewer 0 setAutoRedraw 1
viewer 0 redraw

correlationPanel closeTabs
correlationPanel setTabName 0 "Correlation 1"
correlationPanel 0 setLogScalingOnAxis 0 0
correlationPanel 0 setLogScalingOnAxis 1 0

histogramPanel closeTabs
histogramPanel setTabName 0 "Histogram 1"
histogramPanel 0 setLogScalingOnAxis 0 0
histogramPanel 0 setLogScalingOnAxis 1 1

