Warning, /geant4/examples/advanced/dna/moleculardna/fiber.mac is written in an unsupported language. File is not indexed.
0001 ### Single DNA fiber visualization
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 /material/verbose 2
0015 /dnageom/verbose 1
0016
0017 # Chemistry: selection of IRT_syn
0018 /process/chem/TimeStepModel IRT_syn
0019
0020 # Chemistry: activation
0021 /chem/activate false
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 300 nm
0031
0032 # Geometry: size of cell volume
0033 # See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
0034 /cell/radiusSize 100 100 100 nm
0035
0036 # Geometry: optimisation of voxelisation
0037 /dnageom/setSmartVoxels 1
0038
0039 # Geometry: check overlaps in DNA geometry region
0040 /dnageom/checkOverlaps false
0041
0042 # Geometry: creation
0043 # See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
0044 # - Side length for each placement
0045 /dnageom/placementSize 30 30 100 nm
0046 # - Scaling of XYZ in fractal definition file
0047 /dnageom/fractalScaling 1 1 1 nm
0048 # - Path to file that defines placement locations
0049 /dnageom/definitionFile geometries/prisms1.txt
0050 # - Set a placement volume
0051 /dnageom/placementVolume prism geometries/straight-216-0.txt
0052
0053 # Geometry: take the angles in the voxel placement file as multiples of pi
0054 /dnageom/setVoxelPlacementAnglesAsMultiplesOfPi false
0055
0056 # Geometry: enable custom molecule sizes
0057 /dnageom/useCustomMoleculeSizes false
0058
0059 # Geometry: draw cell/chromosome volumes rather than DNA
0060 /dnageom/drawCellVolumes false
0061
0062 # Geometry: distance from base pairs at which radicals are killed
0063 /dnageom/radicalKillDistance 9 nm
0064
0065 # Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
0066 /dnageom/interactionDirectRange 6 angstrom
0067
0068 # Geometry: activate Histone scavenging function
0069 /dnageom/activateHistoneScavenging true
0070
0071 # Damage: model settings
0072 /dnadamage/directDamageLower 17.5 eV
0073 /dnadamage/directDamageUpper 17.5 eV
0074
0075 /dnadamage/indirectOHBaseChance 1.0
0076 /dnadamage/indirectOHStrandChance 0.65
0077 /dnadamage/inductionOHChance 0.0
0078
0079 /dnadamage/indirectHBaseChance 1.0
0080 /dnadamage/indirectHStrandChance 0.65
0081 /dnadamage/inductionHChance 0.0
0082
0083 /dnadamage/indirectEaqBaseChance 1.0
0084 /dnadamage/indirectEaqStrandChance 0.65
0085 /dnadamage/inductionEaqChance 0.0
0086
0087 # Analysis: add spherical chromosomal region of interest, with the name "fiber"
0088 /chromosome/add fiber sphere 2000 0 0 0 nm
0089
0090 # Analysis: set whether strands ought be saved
0091 /analysisDNA/saveStrands false
0092
0093 # Analysis: gap between DNA fragments in base pair
0094 # Set to zero to score placement volumes independently
0095 /analysisDNA/fragmentGap 0
0096
0097 # Analysis: save the position of hits histones only on one chain
0098 #/analysisDNA/diagnosticChain
0099
0100 # Run: initialization
0101 /run/initialize
0102
0103 # Visualization: to visualize fiber DNA geometry
0104 # - uncomment the next line and save
0105 /control/execute vis.mac
0106 # - then, run ./moleculardna -t 1 -v 1
0107 # - then, in the Session window of the Qt interface, do /control/execute fiber.mac
0108
0109 # Unit tests only
0110 #/dnatests/uniqueid
0111 #/dnatests/basepairs
0112 #/dnatests/chromosome
0113 #/analysisDNA/testClassifier
0114 # End unit tests
0115
0116 # Run: progress display
0117 /run/printProgress 100
0118
0119 # Source geometry
0120 #/gps/pos/type Volume
0121 #/gps/pos/shape Sphere
0122 #/gps/pos/radius 500 nm
0123 #/gps/pos/centre 0 0 0 nm
0124
0125 # Source particle, energy and angular distribution
0126 /gps/particle e-
0127 /gps/energy 100 eV
0128 /gps/ang/type iso
0129
0130 # Beam on
0131 /tracking/verbose 0
0132 /run/beamOn 10
0133
