dna/moleculardna/plasmid.mac

0001 ### Plasmid default geometry
0002
0003 #
0004 # See more details on moleculardna specific UI commands:
0005 # - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
0006 # - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
0007 # - the README file
0008 # - the messenger classes of the moleculardna example
0009 #
0010
0011 # Physics: choice of thermalization model
0012 /process/dna/e-SolvationSubType Meesungnoen2002
0013 #/process/dna/e-SolvationSubType Ritchie1994
0014 #/process/dna/e-SolvationSubType Terrisol1990
0015
0016 # Verbosity: settings
0017 /run/verbose 2
0018 /tracking/verbose 0
0019 /control/verbose 1
0020 /dnageom/verbose 1
0021
0022 # Chemistry: selection of IRT_syn
0023 /process/chem/TimeStepModel IRT_syn
0024
0025 # Chemistry: activation
0026 /chem/activate true
0027
0028 # Chemistry: verbosity
0029 /scheduler/verbose 0
0030
0031 # Material: verbosity
0032 /material/verbose 2
0033
0034 # Geometry: size of World volume
0035 /world/worldSize 4.84 um
0036
0037 # Geometry: optimisation of voxelisation
0038 /dnageom/setSmartVoxels 1
0039 /dnageom/checkOverlaps false
0040
0041 # Geometry: creation
0042 # See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
0043 #  - Side length for each placement
0044 /dnageom/placementSize 200 200 200 nm
0045 #  - Scaling of XYZ in fractal definition file
0046 /dnageom/fractalScaling 1 1 1 nm
0047 #  - Path to file that defines placement locations
0048 /dnageom/definitionFile geometries/prisms_plasmids_positions_500ngpul.txt
0049 #  - Set placement volumes
0050 /dnageom/placementVolume prism geometries/plasmid_4367.txt
0051
0052 # Geometry: take the angles in the voxel placement file as multiples of pi
0053 /dnageom/setVoxelPlacementAnglesAsMultiplesOfPi false
0054
0055 # Geometry: enable custom molecule sizes
0056 /dnageom/useCustomMoleculeSizes false
0057
0058 # Geometry: draw cell/chromosome volumes rather than DNA
0059 /dnageom/drawCellVolumes false
0060
0061 # Geometry: distance from base pairs at which radicals are killed
0062 /dnageom/radicalKillDistance 9 nm
0063
0064 # Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
0065 /dnageom/interactionDirectRange 5.5 angstrom
0066
0067 # Geometry: activate Histone scavenging function
0068 /dnageom/activateHistoneScavenging true
0069
0070 # Analysis: add box chromosomal region of interest, with the name "plasmid"
0071 /chromosome/add plasmid box 2.21 2.21 2.42 0 0 0 um
0072
0073 # Damage: model settings
0074 /dnadamage/directDamageLower 17.5 eV
0075 /dnadamage/directDamageUpper 17.5 eV
0076
0077 /dnadamage/indirectOHBaseChance 1.0
0078 /dnadamage/indirectOHStrandChance 0.65
0079 /dnadamage/inductionOHChance 0.0
0080
0081 /dnadamage/indirectHBaseChance 1.0
0082 /dnadamage/indirectHStrandChance 0.65
0083 /dnadamage/inductionHChance 0.00
0084
0085 /dnadamage/indirectEaqBaseChance 1.0
0086 /dnadamage/indirectEaqStrandChance 0.65
0087 /dnadamage/inductionEaqChance 0.00
0088
0089 # Analysis: set whether strands ought be saved
0090 /analysisDNA/saveStrands false
0091
0092 # Analysis: gap between DNA fragments in base pair
0093 #  Set to zero to score placement volumes independently
0094 /analysisDNA/fragmentGap 0  # do not join
0095
0096 # Draw cell/chromosome volumes rather than DNA (makes DNA invisible)
0097 /dnageom/drawCellVolumes false
0098
0099 # Run: initialization
0100 /run/initialize
0101
0102 # --> Unit tests
0103 #/dnatests/uniqueid
0104 #/dnatests/basepairs
0105 #/dnatests/chromosome
0106 #/analysisDNA/testClassifier
0107 # --> End unit tests
0108
0109 # Run: progress display
0110 /run/printProgress 100
0111
0112 # Source geometry
0113 /gps/pos/type Plane
0114 /gps/pos/shape Square
0115 /gps/pos/centre 0 0 -2.42 um
0116 /gps/pos/halfx 2.21 um
0117 /gps/pos/halfy 2.21 um
0118
0119 # Source particle, energy and angular distribution
0120 /gps/particle proton
0121 /gps/energy 3 MeV
0122 /gps/direction 0 0 1
0123
0124 # Beam on
0125 /run/beamOn 10