[Issue]:Scoring DNA damage on cell nucleus

[LucasHenriqueDG]

Contact Details

No response

What was the issue?

I'm trying to run some simulations, but I've faced some issues related to the DNADamageNucleusStepByStep.
I've successfully made some simulations using the TsNucleus, however, when i try to score the DNA damage of a Nucleus inside a Cell, it doesn't work, is that possible or not?

My Code (I'm adapting the examples):
`# -- Geometry

World

d:Ge/World/HLX = 15.0 um
d:Ge/World/HLY = 15.0 um
d:Ge/World/HLZ = 15.0 um
b:Ge/World/Invisible = "true"
s:Ge/World/Material = "G4_WATER"

s:Ge/MyCell/Type="TsSphericalCell"
s:Ge/MyCell/Material="G4_WATER"
s:Ge/MyCell/Parent="World"
d:Ge/MyCell/CellRadius=10 um
s:Ge/MyCell/Color="white"

s:Ge/MyCell/Nucleus/Type = "TsNucleus"
s:Ge/MyCell/Nucleus/Material = "G4_WATER"
s:Ge/MyCell/Nucleus/Color = "RED"
s:Ge/MyCell/Nucleus/DNAModel = "Sphere"
d:Ge/MyCell/Nucleus/NucleusRadius = 4.65 um
i:Ge/MyCell/Nucleus/HilbertCurveLayer = 4
i:Ge/MyCell/Nucleus/HilbertCurve3DRepeat = 30
s:Ge/MyCell/Nucleus/HilbertCurveFileName = "supportFiles/HilbertPoints_iteration1.dat"
s:Ge/MyCell/Nucleus/Voxel/Material = "G4_WATER"
b:Ge/MyCell/Nucleus/ShowDNAVoxels = "false"
s:Ge/MyCell/Nucleus/ChromatinFiber/Material = "G4_WATER"
b:Ge/MyCell/Nucleus/ShowChromatinCylinders = "false"
s:Ge/MyCell/Nucleus/Histone/Material = "G4_HistoneMaterial"
b:Ge/MyCell/Nucleus/OnlyBuildOneHistone = "false"
b:Ge/MyCell/Nucleus/HistoneAsScavenger = "true"
b:Ge/MyCell/Nucleus/AddBases = "true"
s:Ge/MyCell/Nucleus/Base1/Material = "G4_BaseMaterial"
s:Ge/MyCell/Nucleus/Base2/Material = "G4_BaseMaterial"
b:Ge/MyCell/Nucleus/AddBackbones = "true"
s:Ge/MyCell/Nucleus/Backbone1/Material = "G4_BackboneMaterial"
s:Ge/MyCell/Nucleus/Backbone2/Material = "G4_BackboneMaterial"
b:Ge/MyCell/Nucleus/AddHydrationShell = "true"
s:Ge/MyCell/Nucleus/HydrationShell1/Material = "G4_WATER_MODIFIED"
s:Ge/MyCell/Nucleus/HydrationShell2/Material = "G4_WATER_MODIFIED"

-- Materials

s:Ma/G4_HistoneMaterial/CloneFromMaterial = "G4_WATER"
d:Ma/G4_HistoneMaterial/CloneWithDensity = 1.407 g/cm3
s:Ma/G4_BaseMaterial/CloneFromMaterial = "G4_WATER"
d:Ma/G4_BaseMaterial/CloneWithDensity = 1.0 g/cm3
s:Ma/G4_BackboneMaterial/CloneFromMaterial = "G4_WATER"
d:Ma/G4_BackboneMaterial/CloneWithDensity = 1.0 g/cm3
s:Ma/G4_WATER_MODIFIED/CloneFromMaterial = "G4_WATER"
d:Ma/G4_WATER_MODIFIED/CloneWithDensity = 1.0 g/cm3

-- Physics and Chemistry

sv:Ph/Default/Modules = 1 "g4em-dna"
#sv:Ph/Default/Modules = 2 "g4em-dna" "TsEmDNAChemistry" # OR physics and chemistry
#includeFile = supportFiles/TOPASDefaultReactions.txt
#s:Ch/ChemistryName = "TOPASChemistry"
#b:Ch/TOPASChemistry/ChemicalStageTransportActive = "True"
i:Ph/Verbosity = 0

-- Source and runs

s:So/ParticleGun/Type = "Beam"
s:So/ParticleGun/Component = "BeamPosition"
d:Ge/BeamPosition/TransX = 0.05 um
d:Ge/BeamPosition/TransY = 0.05 um
d:Ge/BeamPosition/TransZ = 4.65 um
s:So/ParticleGun/BeamParticle = "alpha"
s:So/ParticleGun/BeamPositionDistribution = "none" # EITHER single track position
#s:So/ParticleGun/BeamPositionDistribution = "Flat" # OR disk source
#s:So/ParticleGun/BeamPositionCutoffShape = "Ellipse"
#d:So/ParticleGun/BeamPositionCutoffX = Ge/MyCell/Nucleus/NucleusRadius um
#d:So/ParticleGun/BeamPositionCutoffY = Ge/MyCell/Nucleus/NucleusRadius um
s:So/ParticleGun/BeamAngularDistribution = "none"
d:So/ParticleGun/BeamEnergy = 5.0 MeV
i:So/ParticleGun/NumberOfHistoriesInRun = 10
b:Ge/MyCell/Nucleus/RotateNucleusForEachRun = "false"

Producing separate runs instead of separate histories if rotation enabled

#d:Tf/TimelineStart = 0. s
#d:Tf/TimelineEnd = 10. s
#i:Tf/NumberOfSequentialTimes = 5 # Number of runs

-- Scorer --

includeFile = DNAScorerStepByStep.txt
s:Sc/DNADamageScorer/Quantity = "DNADamageNucleusStepByStep"
s:Sc/DNADamageScorer/Component = "MyCell/Nucleus"
i:Sc/DNADamageScorer/NumberOfHistoriesInRun = So/ParticleGun/NumberOfHistoriesInRun
d:Sc/DNADamageScorer/ScoringRadius = Ge/MyCell/Nucleus/NucleusRadius um
i:Sc/DNADamageScorer/BasePairPositionAtGeometricHierarchy = 0
sv:Sc/DNADamageScorer/Strand1MaterialNames = 4 "G4_WATER_MODIFIED" "G4_BackboneMaterial" "G4_BaseMaterial" "G4_HistoneMaterial"
sv:Sc/DNADamageScorer/Strand2MaterialNames = 3 "G4_WATER_MODIFIED" "G4_BackboneMaterial" "G4_BaseMaterial"
s:Sc/DNADamageScorer/PrimaryParticle = So/ParticleGun/BeamParticle
d:Sc/DNADamageScorer/MeanEnergy = So/ParticleGun/BeamEnergy MeV
#d:Sc/DNADamageScorer/StopTrackingAtDose = 0.5 gray
d:Sc/DNADamageScorer/ImageXMinPosition = 0 um - Ge/MyCell/Nucleus/NucleusRadius
d:Sc/DNADamageScorer/ImageXMaxPosition = Ge/MyCell/Nucleus/NucleusRadius um
d:Sc/DNADamageScorer/ImageYMinPosition = 0 um - Ge/MyCell/Nucleus/NucleusRadius
d:Sc/DNADamageScorer/ImageYMaxPosition = Ge/MyCell/Nucleus/NucleusRadius um
d:Sc/DNADamageScorer/ImageZMinPosition = 0 um - Ge/MyCell/Nucleus/NucleusRadius
d:Sc/DNADamageScorer/ImageZMaxPosition = Ge/MyCell/Nucleus/NucleusRadius um
s:Sc/DNADamageScorer/GeometryInfo = "supportFiles/Geoinfo.txt"
s:Sc/DNADamageScorer/CopyNoTable = "supportFiles/CopyNoTable.txt"
s:Sc/DNADamageScorer/FileVoxelCopyNumbersInsideNucleus = "supportFiles/CopyNoTable.txt"
s:Sc/DNADamageScorer/MapChromosomeVoxelsFile = "supportFiles/signedCHVoxel.txt"
s:Sc/DNADamageScorer/signedCHVoxel = "supportFiles/signedCHVoxel.txt"
Ts/ShowHistoryCountAtInterval = 1

#Score dose to cell
s:Sc/CellScorer/Quantity = "DoseToMedium"
s:Sc/CellScorer/Component = "MyCell"
b:Sc/CellScorer/OutputToConsole = "TRUE"
b:Sc/CellScorer/PropagateToChildren = "true"
s:Sc/CellScorer/IfOutputFileAlreadyExists = "overwrite"

#Score in the Cell components
s:Sc/OrganelleScorer/Quantity = "TsNtupleForCell"
s:Sc/OrganelleScorer/Component = "MyCell"
s:Sc/OrganelleScorer/IfOutputFileAlreadyExists = "Overwrite"
s:Sc/OrganelleScorer/OutputType = "ASCII"
s:Sc/OrganelleScorer/OutputFile = "EdepToOrganelles"
b:Sc/OrganelleScorer/PropagateToChildren = "true"

-- Visualization

#s:Gr/ViewA/Type = "OpenGL"
#i:Gr/ViewA/WindowSizeX = 1024
#i:Gr/ViewA/WindowSizeY = 768

Ts/PauseBeforeQuit = "True"

i:Ts/Seed = 2580
i:Ts/NumberOfThreads = -2 # defaults to 1
`

In this case, I'm trying to score the DNA damage of the MyCell/Nucleus, however, when i try this:

s:Sc/DNADamageScorer/Component = "MyCell/Nucleus"

I get this error:
DNADamageScorer has unfound component:MyCell/Nucleus

Version

3.0

What Operative System (OS) are you running on?

Windows (WSL)

Relevant log output

Reading geometry information file...
Reading copy number map file...
Reading chromosome-voxel map file...
Topas is exiting due to a serious error in scoring setup.
DNADamageScorer has unfound component:MyCell/Nucleus

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