Hands-on pdb4dna.
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1 Hands-on pdb4dna Emmanuel Delage Yann Perrot Laboratoire de Physique Corpusculaire de Clermont Ferrand Pôle Physique pour la Santé et l Environnement CNRS/IN2P3 Université Blaise Pascal
2 Hands-on pdb4dna Scope of the application PDB files Integration into Geant4 Algorithm to find the closest atom in DNA Strand breaks Application Directory content Build the example Preparation before run Run with GUI Run in batch mode ROOT analysis 2
3 Hands-on pdb4dna Scope of the application PDB files Integration into Geant4 Algorithm to find the closest atom in DNA Strand breaks Application Directory content Build the example Preparation before run Run with GUI Run in batch mode ROOT analysis 3
4 PDB files - atomistic representation Protein Data Bank files : A way to store and exchange polyatomic structures (proteins, DNA) File describing the 3D structural information of molecules A worlwide free access to files obtained experimentally by crystallography techniques or computed with geometry optimization codes File format : ASCII file.pdb We mainly extract information from ATOM keyword HEADER TRANSFERASE 19-APR-13 4BJP TITLE CRYSTAL STRUCTURE OF E. COLI PENICILLIN BINDING PROTEIN 3 JRNL DOI /JOURNAL.PONE REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION ATOM 265 C ASP A C ATOM 266 O ASP A O ATOM 267 CB ASP A C TER 3106 ALA A END 4
5 PDB files DNA example 1/3 10 base pairs example Molecule level HEADER DNA 10BP EXAMPLE MODEL 1 ATOM 1 O5 A O ATOM 2 C5 A C... ATOM 33 OP1 A O... ATOM 65 P A P... ATOM 445 O5 A O TER 445 A 10 ATOM 446 O5 B O... ATOM 688 C4 B C TER 688 B 20 ENDMDL This file encodes DNA molecule Start molecule Atom coordinates first strand (A) Atom coordinates second strand (B) End molecule 5
6 PDB files DNA example 2/3 10 base pairs example nucleotide level HEADER DNA 10BP EXAMPLE MODEL 1 ATOM 1 O5 A O ATOM 2 C5 A C... ATOM 33 OP1 A O... ATOM 65 P A P... ATOM 445 O5 A O TER 445 A 10 ATOM 446 O5 B O... ATOM 688 C4 B C TER 688 B 20 ENDMDL 6
7 PDB files DNA example 3/3 10 base pairs example atomic level Phosphate group Nucleotide structure Base HEADER DNA 10BP EXAMPLE ATOM 65 P DC A P ATOM 66 OP1 DC A O ATOM 67 OP2 DC A O ATOM 68 O5' DC A O Phosphate group HO O P OH O Sugar O OH N NH 2 Cytosine nucleotide N ATOM 69 C5' DC A C ATOM 70 C4' DC A C ATOM 71 O4' DC A O ATOM 72 C3' DC A C ATOM 73 O3' DC A O ATOM 74 C2' DC A C ATOM 75 C1' DC A C O ATOM 76 N1 DC A N ATOM 77 C2 DC A C ATOM 78 O2 DC A O ATOM 79 N3 DC A N ATOM 80 C4 DC A C ATOM 81 N4 DC A N ATOM 82 C5 DC A C ATOM 83 C6 DC A C... Sugar Base 7
8 Integration into Geant4 (1/2) Pdb4dna example will be provided in the next Geant4 release 10.1 PDB Library Geant4 classes To be implemented Inherited Geant4 classes 8
9 Integration into Geant4 (2/2) DetectorConstruction call PDBlib to construct molecule geometry EventAction compute match between Edep and DNA via Detector construction 9
![Algorithm to find the closest atom 1/2 Goal = allocate energy depositions to an element [sugar, phosphate, base] of nucleotides and then deduce SSB and DSB A bounding box is calculated with atoms](/docs-images/78/77282927/images/10-1.jpg "coordinates No other Geant4 solid is needed for simulation We consider that a sphere is a good approximation to englobe a nucleotide.")
10 Algorithm to find the closest atom 1/2 Goal = allocate energy depositions to an element [sugar, phosphate, base] of nucleotides and then deduce SSB and DSB A bounding box is calculated with atoms coordinates No other Geant4 solid is needed for simulation We consider that a sphere is a good approximation to englobe a nucleotide. A list of spheres representing nucleotides is calculated DNA specific Bounding box List of spheres Energy deposition 10
11 Algorithm to find the closest atom 2/2 : Find the closest nucleotide from the energy deposition inside the two strands : Find the closest atom from the energy deposition - atom by atom inside the selected nucleotide - considering Van der Waals radii : Due to sphere overlapping, find a better match in the next two nucleotides in the list : Return algorithm response: - No DNA hit - DNA hit, return nucleotide ID, DNA strand, group type (sugar, phosphate or base) 11
12 Strand breaks Begin of event: A map for each strand is created to store nucleotide ID and associated energy deposition For each step: If the step is in the bounding volume, increment energy deposition per event Ask to PDBlib to check the step position If the step is in a sugar or a phosphate: get nucleotide ID, strand number, energy deposit, update the map (ID, Edep+=StepEdep) End of event: Compute and store strand breaks Store energy deposit in the bounding volume Edep > threshold in sugarphosphate to get a SSB Distance between 2SSB > distance to get a DSB 12
13 Hands-on pdb4dna Scope of the application PDB files Integration into Geant4 Algorithm to find the closest atom in DNA Strand breaks Application Directory content Build the example Preparation before run Run with GUI Run in batch mode ROOT analysis 13
14 Directory content $ ll /mnt/g4tuto/geant install/share/geant /examples/extended/medical/dna/pdb4dna PDB files Root macro file Macro to run in batch mode Macro to run with GUI 14
15 Build the example (1/2) $ module load geant4/10.01-mt $ cd tutorial $ cp -r /mnt/g4tuto/geant install/share/geant /examples/extended/medical/dna/pdb4dna. $ mkdir pdb4dna-build $ cd pdb4dna-build $ cmake../pdb4dna 15
16 Build the example (1/2) $ make j2 16
17 Preparation before run (1/3) Visit Protein Data Bank website 17
18 Preparation before run (2/3) You can find a file by its name, type, sequence, etc For the tutorial, we look at: 1FZX file : 12 bp DNA strands (run with GUI) 1ZBB file : dinucleosome (run in batch mode) 1FZX 1ZBB (Note that for the tutorial, those PDB files are provided in the pdb4dna directory) «Do you know 1AOI.pdb?» 18
19 Preparation before run (3/3) Description of the molecule References Download the file Online view (require Java) 19
20 Run in GUI (1/4) Due to GUI limitation, if you want to select a file into open file dialog you need to rename the extension from pdb to mac. $ cp file.pdb file.mac Run GUI $./pdb4dna Becarefull, the command will change in the next release to:./pdb4dna -gui 20
21 21
22 Run in GUI (2/4) Load PDB file (.mac) Click on Draw menu, and Try different visualisation 22
23 Run in GUI (3/4) Those screenshots correspond to 1ZBB.pdb (.mac) Visualization of a di-nucleosome (Asymmetric Unit of a tetra-nucleosome) Residue view Atomistic view Barycenter view 23
24 Run in GUI (4/4) Launch a simulation configured by runingui.mac in the Run menu Call run and gun commands in the session text box /gun/particle e- /gun/energy 10 kev /run/beamon 10 24
25 Run in batch mode (1/2) 1. Prepare your macro file tutorial.in using your favorite editor (geany ) You can start from the pdb4dna.in macro file turorial.in /run/initialize /PDB4DNA/det/loadPDB 1ZBB.pdb /PDB4DNA/det/buildBoundingV /PDB4DNA/event/setEnergyThres 8.22 ev /PDB4DNA/event/setDistanceThres 10 Select your PDB file Construct the bounding volume Set thresholds for strand breaks: energy, distance /gun/particle proton /gun/energy 1 kev /run/initialize /run/beamon Set characteristics of primaries Initialize and run the simulation 25
26 2. Run the simulation Run in batch mode (2/2) $./pdb4dna m <your_macro_file> -t <number of threads> Becarefull, the command will change to:./pdb4dna mac yourmacrofile mt numberofthread $./pdb4dna m tutorial.in t 2 26
27 Hands-on pdb4dna Scope of the application PDB files Integration into Geant4 Algorithm to find the closest atom in DNA Strand breaks Application Directory content Build the example Preparation before run Run with GUI Run in batch mode ROOT analysis 27
28 ROOT analysis A simulation will produce a root file pdb4dna_output.root 3 histograms: energy deposits in the bounding volume per event, SSB and DSB $ root analysis.c ******************************************* * * * W E L C O M E to R O O T * * * * Version 5.32/04 13 July 2012 * * * * You are welcome to visit our Web site * * * * * ******************************************* ROOT 5.32/04 (tags/v @45051, Jul , 15:55:10 on linuxx8664gcc) CINT/ROOT C/C++ Interpreter version , July 2, 2010 Type? for help. Commands must be C++ statements. Enclose multiple statements between { }. root [0] Processing analysis.c... -> Edep in the target : MeV -> Number of SSB : > Number of DSB : 60 root [1] 28
29 Go further Now, you have an overview of pdb4dna. Your feedback is important. Contact us, we will provide you information concerning technical aspect, implementation, possible improvements Thanks a lot and thanks to the organizers! 29
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