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0001 =================================================================
0002 Geant4 - pdb4dna
0003 =================================================================
0004
0005
0006 Authors: E. Delage *(a), Y. Perrot *(a), Q.T. Pham (a)
0007
0008 (a) Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France
0009 * Corresponding authors, email to delage@clermont.in2p3.fr, perrot@clermont.in2p3.fr
0010
0011 This example is provided by the Geant4-DNA collaboration.
0012
0013 These processes and models are further described at:
0014 http://geant4-dna.org
0015
0016 Any report or published results obtained using the Geant4-DNA software shall
0017 cite the following Geant4-DNA collaboration publications:
0018 Phys. Med. 31 (2015) 861-874
0019 Med. Phys. 37 (2010) 4692-4708
0020
0021 ---> 1. A brief description
0022
0023 The PDB4DNA example simulates energy deposits in a target volume generated from a PDB file representing DNA geometry.
0024 Position of energy deposits are used to compute strand breaks in the DNA geometry.
0025 Geant4-DNA processes are used.
0026
0027 The example package contains:
0028 - source files (src, include, pdb4dna.cc)
0029 - README
0030 - .in, analysis.C and visualization macro files
0031 - 1ZBB.pdb (di nucleosome is loaded by default)
0032
0033 To run the example: see section 4 of this README
0034 To analyze output: see section 6 of this README
0035
0036 ----> 2. Set-up.
0037
0038 The geometry is a 1000 angstrom side cube (World) made of galactic material.
0039 Before a computation, user loads a PDB file and generates a target volume (the bounding volume) of liquid water, which dimensions are extrapolated from PDB file atom 3D coordinates.
0040
0041 ----> 3. Some main features
0042
0043 | MESSENGER LIST |
0044 -----------------------------------------------------------------
0045 [1] Load a PDB file (The default atoms visualization is done by sphere that are parametrized with the van der Waals radius).
0046 CPK coloring.
0047 - Hydrogen(H) => white sphere,
0048 - Carbon(C) => gray sphere,
0049 - Oxygen(O) => red sphere,
0050 - Nitrogen(N) => dark blue sphere,
0051 - Sulfur(S) => yellow sphere,
0052 - Phosphorus(P) => orange sphere,
0053 - others/undefined => pink sphere.
0054 /PDB4DNA/det/loadPDB filename.pdb
0055 -----------------------------------------------------------------
0056 [2] Build only a bounding volume for computation and draw it :
0057 /PDB4DNA/det/buildBoundingV
0058 -----------------------------------------------------------------
0059 [3] Draw Atoms : /PDB4DNA/det/drawAtoms
0060 [4] Draw Nucleotids (sphere representing nucleotids) : /PDB4DNA/det/drawNucleotides
0061 [5] Draw Residues
0062 - Base => blue sphere,
0063 - Sugar => yellow sphere,
0064 - Phosphate => red sphere.
0065 Spheres are linked by cylinders:
0066 /PDB4DNA/det/drawResidues
0067 [6] Draw Atoms with bounding volume : /PDB4DNA/det/drawAtomsWithBounding
0068 [7] Draw Nucleotides with bounding volume : /PDB4DNA/det/drawNucleotidesWithBounding
0069 [8] Draw Residues with bounding volume : /PDB4DNA/det/drawResiduesWithBounding
0070 -----------------------------------------------------------------
0071 [9] Set energy treshold to compute SSB : /PDB4DNA/event/setEnergyThres 8.22 eV (default value set to 8.22 eV)
0072 [10] Set distance treshlod to compute DSB : /PDB4DNA/event/setDistanceThres 10 (default value set to 10)
0073
0074 Notes:
0075 [1] is mandatory for visualization and simulation.
0076 [2] is needed for simulation.
0077
0078 ----> 4. How to run the example.
0079
0080 To get help, run:
0081
0082 > ./pdb4dna(.exe) -h
0083
0084 In interactive mode, run:
0085
0086 > ./pdb4dna(.exe) -gui
0087
0088 "1ZBB.pdb" is the default file and it should be placed into same directory as the executable.
0089 You can download it here:
0090 http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1ZBB
0091
0092 In batch mode , run:
0093
0094 > ./pdb4dna(.exe) [-mac pdb4dna.in] [-mt numberofThreads]
0095
0096 To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro.
0097
0098 ----> 5. The physics
0099
0100 This example shows how to use the Geant4-DNA processes from constructor
0101
0102 Look at the PhyscisList.cc file.
0103
0104 ----> 6. Simulation output
0105
0106 The output results consists in a pdb_dna.root file, containing for each event:
0107 - the energy deposit in the bounding box (in electronVolt)
0108 - the number of single strand break (SSB)
0109 - the number of double strand break (DSB)
0110
0111 This file can be easily analyzed using for example the provided ROOT macro
0112 file analysis.C; to do so :
0113 * be sure to have ROOT installed on your machine
0114 * be sure to be in the example directory
0115 * launch ROOT by typing root
0116 * under your ROOT session, type in : .X analysis.C to execute the macro file
0117 * alternatively you can type directly under your session : root analysis.C
0118
0119 ----> 7. Contacts
0120
0121 If you have any questions or wish to notify of updates and/or modification please contact:
0122
0123 E. Delage (geometry and visualization referee) at delage@clermont.in2p3.fr
0124 Y. Perrot (physics and simulation referee) at perrot@clermont.in2p3.fr
0125
0126
0127 ----> Acknowledgments :
0128
0129 Jean Orloff (LPC, Clermont-Ferrand, France) for 3D rotation implementation,
0130 Michel Maire (G4AI) for /extended/geometry/transforms example,
0131 Laurent Garnier (LAL, Orsay, France) for Qt visualisation.
0132
0133
