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0001 ############################################## Macro file for Analysis ##############################################
0002 #
0003 #============================================ PARAMETERS FOR DAMAGES ============================================
0004 #" **Note: "#" is used for comments. Thereby, remove the "#" at the beginning of folowing commands to use them.
0005 #/ana/cellNucleusName Fibroblast # Optional;
0006 #/ana/ouputName Output0.dat #Set name for output file, default is Output.dat
0007 #/ana/folderForChemOut chem_output #Set folder that contains outputs of chemical stage, default: chem_output
0008 #/ana/thresholdFordirectSBSelection 17.5 # eV; Threshold for selecting direct damages; default value is 17.5 eV
0009 #/ana/probForIndirectSBSelection 40 # %; Propability for selecting indirect damages; default value is 40 %
0010 #/ana/skipIndirectDamages # Use it if users want to skip analyzing indirect damages
0011
0012 #
0013 #======================================= PARAMETERS FOR CLASSIFYING DAMAGES =======================================
0014 #
0015 ## **Note: For classifying damages, repair models (TLK, LEMIV..), user can load damages from an existing SDD file.
0016 #/ana/loadDamagesFromSDD SDDformat_Output.dat #load damages from existing SDD file. It'll skip analyzing root files.
0017 #/ana/BpForDSB 10 # The minimum distance between two clusters, default value is 10
0018 #/ana/unitOfNormalization 2 #unit type for normization: 1: [Gy-1 * Gbp-1]; 2 : [Gy-1]; default is 1
0019
0020 #
0021 #============================================ PARAMETERS FOR TLK MODEL ============================================
0022 #
0023 /ana/TLK/used true #flag to enable/disable TLK model. Enabled if: true
0024 /ana/TLK/lambda1 3.0 #λ1 and λ2 are respectively simple DSB and complex repair probability
0025 /ana/TLK/lambda2 0.03 #λ1 and λ2 are respectively simple DSB and complex repair probability
0026 /ana/TLK/beta1 0.01 #β1 and β2 are respectively simple DSB and complex misrepair probability
0027 /ana/TLK/beta2 0.06 #β1 and β2 are respectively simple DSB and complex misrepair probability
0028 /ana/TLK/eta 0.0002 # h-1;a binary misrepair probability ; 0.0011 for DNAFabric fibroblast
0029 #/ana/TLK/eta 0.0011 # h-1;a binary misrepair probability; 0.0011 for DNAFabric fibroblast
0030 /ana/TLK/doseMax 6.0 #Compute SF up to doseMax Gy and with step deltaDose
0031 /ana/TLK/deltaDose 0.25 #Compute SF up to doseMax Gy and with step deltaDose
0032
0033 #
0034 #============================================ PARAMETERS FOR LEMIV MODEL ============================================
0035 #
0036 /ana/LEMIV/used true #flag to enable/disable LEMIV model. Enabled if: true
0037 #/ana/LEMIV/loopLength 2E6 #length of the loop in bp, default 2Mbp
0038 /ana/LEMIV/Funrej 0 #Funrej is the fraction of DSBs that are not repaired even for late times
0039 /ana/LEMIV/Tfast 0.24 #constant time in h-1
0040 /ana/LEMIV/Tslow 2.81 #constant time in h-1
0041 /ana/LEMIV/timeMax 25 # compute fraction of unrejoined DSB up to timeMax h at deltaT step
0042 /ana/LEMIV/deltaTime 0.25 # compute fraction of unrejoined DSB up to timeMax h at deltaT step
0043 #
0044 #============================================ PARAMETERS FOR BELOV MODEL ============================================
0045 # **Note: The implementation of BELOV model in dsbandrepair is still in development
0046 /ana/BELOV/used false #flag to enable/disable BELOV model. Enabled if: true
0047 /ana/BELOV/Nirrep 0.035 #Nirrep fraction, if it's not be set, fraction of complex DSB will be used
0048 /ana/BELOV/Dz 1.0 #Dz
