Warning, /geant4/examples/advanced/dna/moleculardna/ecoli.mac is written in an unsupported language. File is not indexed.
0001 ### E. coli bacterium
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 # Verbosity: settings
0012 /control/verbose 1
0013 /run/verbose 2
0014 /dnageom/verbose 1
0015 #/tracking/verbose 2
0016
0017 # Chemistry: selection of IRT_syn
0018 /process/chem/TimeStepModel IRT_syn
0019
0020 # Chemistry: activation
0021 /chem/activate true
0022
0023 # Chemistry: verbosity
0024 /scheduler/verbose 0
0025
0026 # Chemistry: end time of chemistry stage
0027 /scheduler/endTime 1 us
0028
0029 # Geometry: size of World volume
0030 /world/worldSize 8 um
0031
0032 # Geometry: optimisation of voxelisation
0033 /dnageom/setSmartVoxels 1
0034
0035 # Geometry: creation
0036 # See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
0037 # - Side length for each placement
0038 /dnageom/placementSize 50 50 50 nm
0039 # - Scaling of XYZ in fractal definition file
0040 /dnageom/fractalScaling 50 50 50 nm
0041 # - Path to file that defines placement locations
0042 /dnageom/definitionFile geometries/bacteria-XFXFXFX-4.txt
0043 # - Set placement volumes
0044 /dnageom/placementVolume turn geometries/8strands_50nm_turn.txt
0045 /dnageom/placementVolume turntwist geometries/8strands_50nm_turn.txt true
0046 /dnageom/placementVolume straight geometries/8strands_50nm_straight.txt
0047
0048 # Geometry: distance from base pairs at which radicals are killed
0049 /dnageom/radicalKillDistance 4 nm
0050
0051 # Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
0052 /dnageom/interactionDirectRange 6 angstrom
0053
0054 # Damage: model settings
0055 /dnadamage/directDamageLower 17.5 eV
0056 /dnadamage/directDamageUpper 17.5 eV
0057
0058 /dnadamage/indirectOHBaseChance 1.0
0059 /dnadamage/indirectOHStrandChance 0.4
0060 /dnadamage/inductionOHChance 0.
0061
0062 /dnadamage/indirectHBaseChance 1.0
0063 /dnadamage/indirectHStrandChance 0.4
0064 /dnadamage/inductionHChance 0.0
0065
0066 /dnadamage/indirectEaqBaseChance 1.0
0067 /dnadamage/indirectEaqStrandChance 0.4
0068 /dnadamage/inductionEaqChance 0.0
0069
0070 # Analysis: add ellipsoid chromosomal region of interest, with the name "bacteria"
0071 /chromosome/add bacteria ellipse 900 400 400 0 0 0 nm 0 0 0
0072
0073 # Analysis: save plot data to specified file
0074 #/chromosome/plotData chromosome.txt
0075
0076 # Tests of geometry
0077 #/dnatests/chromosome
0078
0079 # Analysis: save strands in given directory
0080 /analysisDNA/saveStrands false
0081 /analysisDNA/strandDir ./damage_maps/
0082
0083 # Run: initialization
0084 /run/initialize
0085
0086 # Tests of geometry
0087 /dnatests/uniqueid
0088 /dnatests/basepairs
0089
0090 # Run: progress display
0091 /run/printProgress 1
0092
0093 # Source geometry
0094 /gps/pos/type Surface
0095 /gps/pos/shape Ellipsoid
0096 /gps/pos/centre 0 0 0 nm
0097 /gps/pos/halfx 900 nm
0098 /gps/pos/halfy 400 nm
0099 /gps/pos/halfz 400 nm
0100 /gps/ang/type cos
0101
0102 # Source particle and energy
0103 /gps/particle e-
0104 /gps/energy 9.999 keV
0105
0106 # Beam on
0107 /run/beamOn 500
