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:
geant4-dna.org">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:
www.rcsb.org/pdb/download/downloadFile.do">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.
...
SEE ALSO: README
