================================================================= Geant4 - pdb4dna ================================================================= Authors: E. Delage *(a), Y. Perrot *(a), Q.T. Pham (a) (a) Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France * Corresponding authors, email to delage@clermont.in2p3.fr, perrot@clermont.in2p3.fr 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: Phys. Med. 31 (2015) 861-874 Med. Phys. 37 (2010) 4692-4708 ---> 1. 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 To analyze output: see section 6 of this README ----> 2. 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. ----> 3. 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). CPK coloring. - 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. /PDB4DNA/det/loadPDB filename.pdb ----------------------------------------------------------------- [2] Build only a bounding volume for computation and draw it : /PDB4DNA/det/buildBoundingV ----------------------------------------------------------------- [3] Draw Atoms : /PDB4DNA/det/drawAtoms [4] Draw Nucleotids (sphere representing nucleotids) : /PDB4DNA/det/drawNucleotides [5] Draw Residues - Base => blue sphere, - Sugar => yellow sphere, - Phosphate => red sphere. Spheres are linked by cylinders: /PDB4DNA/det/drawResidues [6] Draw Atoms with bounding volume : /PDB4DNA/det/drawAtomsWithBounding [7] Draw Nucleotides with bounding volume : /PDB4DNA/det/drawNucleotidesWithBounding [8] Draw Residues with bounding volume : /PDB4DNA/det/drawResiduesWithBounding ----------------------------------------------------------------- [9] Set energy treshold to compute SSB : /PDB4DNA/event/setEnergyThres 8.22 eV (default value set to 8.22 eV) [10] Set distance treshlod to compute DSB : /PDB4DNA/event/setDistanceThres 10 (default value set to 10) Notes: [1] is mandatory for visualization and simulation. [2] is needed for simulation. ----> 4. 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: 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] To get visualization, make sure to uncomment the #/control/execute vis.mac line in the macro. ----> 5. The physics This example shows how to use the Geant4-DNA processes from constructor Look at the PhyscisList.cc file. ----> 6. Simulation output The output results consists in a pdb_dna.root file, containing for each event: - the energy deposit in the bounding box (in electronVolt) - the number of single strand break (SSB) - the number of double strand break (DSB) This file can be easily analyzed using for example the provided ROOT macro file analysis.C; to do so : * be sure to have ROOT installed on your machine * be sure to be in the example directory * launch ROOT by typing root * under your ROOT session, type in : .X analysis.C to execute the macro file * alternatively you can type directly under your session : root analysis.C ----> 7. Contacts If you have any questions or wish to notify of updates and/or modification please contact: E. Delage (geometry and visualization referee) at delage@clermont.in2p3.fr Y. Perrot (physics and simulation referee) at perrot@clermont.in2p3.fr ----> Acknowledgments : Jean Orloff (LPC, Clermont-Ferrand, France) for 3D rotation implementation, Michel Maire (G4AI) for /extended/geometry/transforms example, Laurent Garnier (LAL, Orsay, France) for Qt visualisation.