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_Geant4 Version:_11.3.0
_Operating System:_Red Hat Enterprise Linux 8.7 (Ootpa)
_Compiler/Version:_gcc-11.3.0
_CMake Version:_3.23.1
I am working on simulating plasmid DNA damage (e.g., pUC19) using the MolecularDNA example. The provided example includes geometry for a plasmid named plasmid_4367. However, I need to generate a similar structure for a different plasmid. I have been exploring the FractalDNA package, but I couldn’t find a suitable DNA model for plasmids. Could you suggest any methods, tools, or workflows to create custom plasmid structures for use in the MolecularDNA example?
Basically, plasmide under supercoil forme is a ramdom circle with the lenght of DNA base paire. You may need to generate this forme according to number of DNA base paire you want. The FractalDNA package can help you to fill dna geometry in this forme. If you cannot creat your pUC19, a example of this plasmide can be found in dnaddamage2. Good luck!
Thank you for your response. I reviewed the dnadamage2 example, and while it does provide the pUC19 plasmid structure as XYZ coordinates, the moleculardna example requires a different format. Specifically, the required format includes:
#NAME
SHAPE
CHAIN_ID
STRAND_ID
BP_INDEX
SIZE_X
SIZE_Y
SIZE_Z
POS_X
POS_Y
POS_Z
ROT_X
ROT_Y
ROT_Z
Phosphate
sphere
0
0
0
2.282353867
2.282353867
2.282353867
151.8451065
436.6706005
108.1613349
2.235297161
0.176505727
0.948744205
Sugar
sphere
0
0
0
2.632139826
2.632139826
2.632139826
151.8609782
440.107885
106.5634079
2.235297161
0.176505727
0.948744205
I am currently facing challenges in converting or generating the XYZ coordinates into this required format. While the fractaldna package provides tools to create structures using fractal or solenoidal shapes, I haven’t found a way to generate the exact format needed for the pUC19 plasmid or from any XYZ coordinate.
Is there a specific tool or method you would recommend for this task?