Author: E. Delage, Y. Perrot, Q.T. Pham
Laboratoire de Physique Corpusculaire de Clermont-Ferrand
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: Phys. Med. 31 (2015) 861-874 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 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:
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.

The physics

This example shows how to use the Geant4-DNA processes from constructor

Look at the PhyscisList.cc file.

Simulation output

The output results consists in a pdb.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

Contacts

If you have any questions or wish to notify of updates and/or modification please contact:
E. Delage (geometry and visualization referee) at delag.nosp@m.e@cl.nosp@m.ermon.nosp@m.t.in.nosp@m.2p3.f.nosp@m.r
Y. Perrot (physics and simulation referee) at perro.nosp@m.t@cl.nosp@m.ermon.nosp@m.t.in.nosp@m.2p3.f.nosp@m.r

-—> 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.