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?
Thank you for your assistance!
AK