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1 =================================================================
2 Geant4 - pdb4dna
3 =================================================================
4
5
6 Authors: E. Delage *(a), Y. Perrot *(a), Q.T. Pham (a)
7
8 (a) Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France
9 * Corresponding authors, email to delage@clermont.in2p3.fr, perrot@clermont.in2p3.fr
10
11 This example is provided by the Geant4-DNA collaboration.
12
13 These processes and models are further described at:
14 http://geant4-dna.org
15
16 Any report or published results obtained using the Geant4-DNA software shall
17 cite the following Geant4-DNA collaboration publications:
18 Phys. Med. 31 (2015) 861-874
19 Med. Phys. 37 (2010) 4692-4708
20
21 ---> 1. A brief description
22
23 The PDB4DNA example simulates energy deposits in a target volume generated from a PDB file representing DNA geometry.
24 Position of energy deposits are used to compute strand breaks in the DNA geometry.
25 Geant4-DNA processes are used.
26
27 The example package contains:
28 - source files (src, include, pdb4dna.cc)
29 - README
30 - .in, analysis.C and visualization macro files
31 - 1ZBB.pdb (di nucleosome is loaded by default)
32
33 To run the example: see section 4 of this README
34 To analyze output: see section 6 of this README
35
36 ----> 2. Set-up.
37
38 The geometry is a 1000 angstrom side cube (World) made of galactic material.
39 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.
40
41 ----> 3. Some main features
42
43 | MESSENGER LIST |
44 -----------------------------------------------------------------
45 [1] Load a PDB file (The default atoms visualization is done by sphere that are parametrized with the van der Waals radius).
46 CPK coloring.
47 - Hydrogen(H) => white sphere,
48 - Carbon(C) => gray sphere,
49 - Oxygen(O) => red sphere,
50 - Nitrogen(N) => dark blue sphere,
51 - Sulfur(S) => yellow sphere,
52 - Phosphorus(P) => orange sphere,
53 - others/undefined => pink sphere.
54 /PDB4DNA/det/loadPDB filename.pdb
55 -----------------------------------------------------------------
56 [2] Build only a bounding volume for computation and draw it :
57 /PDB4DNA/det/buildBoundingV
58 -----------------------------------------------------------------
59 [3] Draw Atoms : /PDB4DNA/det/drawAtoms
60 [4] Draw Nucleotids (sphere representing nucleotids) : /PDB4DNA/det/drawNucleotides
61 [5] Draw Residues
62 - Base => blue sphere,
63 - Sugar => yellow sphere,
64 - Phosphate => red sphere.
65 Spheres are linked by cylinders:
66 /PDB4DNA/det/drawResidues
67 [6] Draw Atoms with bounding volume : /PDB4DNA/det/drawAtomsWithBounding
68 [7] Draw Nucleotides with bounding volume : /PDB4DNA/det/drawNucleotidesWithBounding
69 [8] Draw Residues with bounding volume : /PDB4DNA/det/drawResiduesWithBounding
70 -----------------------------------------------------------------
71 [9] Set energy treshold to compute SSB : /PDB4DNA/event/setEnergyThres 8.22 eV (default value set to 8.22 eV)
72 [10] Set distance treshlod to compute DSB : /PDB4DNA/event/setDistanceThres 10 (default value set to 10)
73
74 Notes:
75 [1] is mandatory for visualization and simulation.
76 [2] is needed for simulation.
77
78 ----> 4. How to run the example.
79
80 To get help, run:
81
82 > ./pdb4dna(.exe) -h
83
84 In interactive mode, run:
85
86 > ./pdb4dna(.exe) -gui
87
88 "1ZBB.pdb" is the default file and it should be placed into same directory as the executable.
89 You can download it here:
90 http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1ZBB
91
92 In batch mode , run:
93
94 > ./pdb4dna(.exe) [-mac pdb4dna.in] [-mt numberofThreads]
95
96 To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro.
97
98 ----> 5. The physics
99
100 This example shows how to use the Geant4-DNA processes from constructor
101
102 Look at the PhyscisList.cc file.
103
104 ----> 6. Simulation output
105
106 The output results consists in a pdb_dna.root file, containing for each event:
107 - the energy deposit in the bounding box (in electronVolt)
108 - the number of single strand break (SSB)
109 - the number of double strand break (DSB)
110
111 This file can be easily analyzed using for example the provided ROOT macro
112 file analysis.C; to do so :
113 * be sure to have ROOT installed on your machine
114 * be sure to be in the example directory
115 * launch ROOT by typing root
116 * under your ROOT session, type in : .X analysis.C to execute the macro file
117 * alternatively you can type directly under your session : root analysis.C
118
119 ----> 7. Contacts
120
121 If you have any questions or wish to notify of updates and/or modification please contact:
122
123 E. Delage (geometry and visualization referee) at delage@clermont.in2p3.fr
124 Y. Perrot (physics and simulation referee) at perrot@clermont.in2p3.fr
125
126
127 ----> Acknowledgments :
128
129 Jean Orloff (LPC, Clermont-Ferrand, France) for 3D rotation implementation,
130 Michel Maire (G4AI) for /extended/geometry/transforms example,
131 Laurent Garnier (LAL, Orsay, France) for Qt visualisation.
132
133
