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 \page ExamplePdb4dna Example pdb4dna
 
 \author E. Delage, Y. Perrot, Q.T. Pham \n
 Laboratoire de Physique Corpusculaire de Clermont-Ferrand \n
 CNRS/IN2P2 - Clermont University, France
 
 This example is provided by the Geant4-DNA collaboration.
 
 These processes and models are further described at:
 http://geant4-dna.org
 
 Any report or published results obtained using the Geant4-DNA software shall 
 cite the following Geant4-DNA collaboration publications: \n
 Phys. Med. 31 (2015) 861-874 \n
 Med. Phys. 37 (2010) 4692-4708
 
 ## A brief description
 
 The PDB4DNA example simulates energy deposits in a target volume generated from a PDB file representing DNA geometry.
 Position of energy deposits are used to compute strand breaks in the DNA geometry.
 Geant4-DNA processes are used. 
 
 The example package contains:
 - source files (src, include, pdb4dna.cc)
 - README
 - .in, analysis.C and visualization macro files
 - 1ZBB.pdb (di nucleosome is loaded by default)
 
 To run the example: see section 4 of this README \n
 To analyze output: see section 6 of this README
 
 ## Set-up
 
 The geometry is a 1000 angstrom side cube (World) made of galactic material.
 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.
 
 ## Some main features
 
 ```
 | MESSENGER LIST |
 -----------------------------------------------------------------
 [1] Load a PDB file (The default atoms visualization is done by sphere that are parametrized with the van der Waals radius). \n
 CPK coloring. \n
 - Hydrogen(H) => white sphere,
 - Carbon(C) => gray sphere,
 - Oxygen(O) => red sphere,
 - Nitrogen(N) => dark blue sphere,
 - Sulfur(S) => yellow sphere,
 - Phosphorus(P) => orange sphere,
 - others/undefined => pink sphere. \n
 /PDB4DNA/det/loadPDB filename.pdb
 -----------------------------------------------------------------
 [2] Build only a bounding volume for computation and draw it : \n
 /PDB4DNA/det/buildBoundingV
 -----------------------------------------------------------------
 [3] Draw Atoms :  /PDB4DNA/det/drawAtoms \n
 [4] Draw Nucleotids (sphere representing nucleotids) :  /PDB4DNA/det/drawNucleotides \n
 [5] Draw Residues : /PDB4DNA/det/drawResidues \n
 - Base => blue sphere,Sugar => yellow sphere,Phosphate => red sphere. \n
 Spheres are linked by cylinders
 
 [6] Draw Atoms with bounding volume : /PDB4DNA/det/drawAtomsWithBounding \n
 [7] Draw Nucleotides with bounding volume : /PDB4DNA/det/drawNucleotidesWithBounding \n
 [8] Draw Residues with bounding volume : /PDB4DNA/det/drawResiduesWithBounding \n
 -----------------------------------------------------------------
 [9] Set energy treshold to compute SSB : /PDB4DNA/event/setEnergyThres 8.22 eV (default value set to 8.22 eV) \n
 [10] Set distance treshlod to compute DSB : /PDB4DNA/event/setDistanceThres 10    (default value set to 10) \n
 
 Notes: \n
 [1] is mandatory for visualization and simulation. \n
 [2] is needed for simulation. \n
 ```
 
 ## How to run the example.
 
 To get help, run:
 
 > ./pdb4dna(.exe) -h
 
 In interactive mode, run:
 
 > ./pdb4dna(.exe) -gui
 
 "1ZBB.pdb" is the default file and it should be placed into same directory as the executable.
 You can download it here: \n
 http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1ZBB
 
 In batch mode , run:
 
 > ./pdb4dna(.exe) [-mac pdb4dna.in] [-mt numberofThreads] \n
 
 To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro.
 
 ## The physics
 
  This example shows how to use the Geant4-DNA processes from constructor
 
 Look at the PhysicsList class.
 
 ## Simulation output
 
 The output results consists in a pdb.root file, containing for each event: \n
 - the energy deposit in the bounding box (in electronVolt) \n
 - the number of single strand break (SSB) \n
 - the number of double strand break (DSB) \n
 
 This file can be easily analyzed using for example the provided ROOT macro 
 file analysis.C; to do so : \n
 * be sure to have ROOT installed on your machine \n
 * be sure to be in the example directory \n
 * launch ROOT by typing root \n
 * under your ROOT session, type in : .X analysis.C to execute the macro file \n
 * alternatively you can type directly under your session : root analysis.C \n
 
 ## Contacts
 
 
 If you have any questions or wish to notify of updates and/or modification please contact: \n
         
 E. Delage (geometry and visualization referee) at delage@clermont.in2p3.fr \n
 Y. Perrot (physics and simulation referee) at perrot@clermont.in2p3.fr
 
 
 ----> Acknowledgments :
 
  Jean Orloff (LPC, Clermont-Ferrand, France) for 3D rotation implementation, \n
  Michel Maire (G4AI) for /extended/geometry/transforms example, \n
  Laurent Garnier (LAL, Orsay, France) for Qt visualisation.

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