Gabriele Cosmo
134 lines
3.6 KiB
Plaintext
134 lines
3.6 KiB
Plaintext
### Single DNA fiber visualization
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#
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# See more details on moleculardna specific UI commands:
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# - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
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# - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
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# - the README file
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# - the messenger classes of the moleculardna example
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#
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# Verbosity: settings
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/control/verbose 1
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/run/verbose 2
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/material/verbose 2
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/dnageom/verbose 1
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# Chemistry: selection of IRT_syn
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/process/chem/TimeStepModel IRT_syn
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# Chemistry: activation
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/chem/activate false
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# Chemistry: verbosity
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/scheduler/verbose 0
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# Chemistry: end time of chemistry stage
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/scheduler/endTime 1 us
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# Geometry: size of World volume
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/world/worldSize 300 nm
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# Geometry: size of cell volume
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# See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
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/cell/radiusSize 100 100 100 nm
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# Geometry: optimisation of voxelisation
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/dnageom/setSmartVoxels 1
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# Geometry: check overlaps in DNA geometry region
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/dnageom/checkOverlaps false
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# Geometry: creation
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# See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
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# - Side length for each placement
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/dnageom/placementSize 30 30 100 nm
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# - Scaling of XYZ in fractal definition file
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/dnageom/fractalScaling 1 1 1 nm
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# - Path to file that defines placement locations
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/dnageom/definitionFile geometries/prisms1.txt
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# - Set a placement volume
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/dnageom/placementVolume prism geometries/straight-216-0.txt
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# Geometry: take the angles in the voxel placement file as multiples of pi
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/dnageom/setVoxelPlacementAnglesAsMultiplesOfPi false
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# Geometry: enable custom molecule sizes
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/dnageom/useCustomMoleculeSizes false
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# Geometry: draw cell/chromosome volumes rather than DNA
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/dnageom/drawCellVolumes false
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# Geometry: distance from base pairs at which radicals are killed
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/dnageom/radicalKillDistance 9 nm
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# Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
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/dnageom/interactionDirectRange 6 angstrom
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# Geometry: activate Histone scavenging function
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/dnageom/activateHistoneScavenging true
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# Damage: model settings
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/dnadamage/directDamageLower 17.5 eV
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/dnadamage/directDamageUpper 17.5 eV
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/dnadamage/indirectOHBaseChance 1.0
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/dnadamage/indirectOHStrandChance 0.65
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/dnadamage/inductionOHChance 0.0
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/dnadamage/indirectHBaseChance 1.0
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/dnadamage/indirectHStrandChance 0.65
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/dnadamage/inductionHChance 0.0
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/dnadamage/indirectEaqBaseChance 1.0
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/dnadamage/indirectEaqStrandChance 0.65
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/dnadamage/inductionEaqChance 0.0
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# Analysis: add spherical chromosomal region of interest, with the name "fiber"
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/chromosome/add fiber sphere 2000 0 0 0 nm
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# Analysis: set whether strands ought be saved
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/analysisDNA/saveStrands false
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# Analysis: gap between DNA fragments in base pair
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# Set to zero to score placement volumes independently
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/analysisDNA/fragmentGap 0
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# Analysis: save the position of hits histones only on one chain
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#/analysisDNA/diagnosticChain
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# Run: initialization
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/run/initialize
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# Visualization: to visualize fiber DNA geometry
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# - uncomment the next line and save
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/control/execute vis.mac
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# - then, run ./moleculardna -t 1 -v 1
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# - then, in the Session window of the Qt interface, do /control/execute fiber.mac
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# Unit tests only
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#/dnatests/uniqueid
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#/dnatests/basepairs
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#/dnatests/chromosome
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#/analysisDNA/testClassifier
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# End unit tests
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# Run: progress display
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/run/printProgress 100
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# Source geometry
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#/gps/pos/type Volume
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#/gps/pos/shape Sphere
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#/gps/pos/radius 500 nm
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#/gps/pos/centre 0 0 0 nm
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# Source particle, energy and angular distribution
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/gps/particle e-
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/gps/energy 100 eV
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/gps/ang/type iso
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# Beam on
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/tracking/verbose 0
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/run/beamOn 10
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