Data extraction and example files for coarse-grained DNA/RNA folding model
- The newest version of oxDNA_analysis_tools (you need to clone from github and run
python -m pip install .). - numpy
Set the directory of the structure you would like to coarse-grain in the dirname variable of get_viz.ipynb and then run all cells
This will generate a couple different visualization/simulation options. First is an xyz file that contains the centers of mass for the individual domains. These files are terrible for visualization (and require a hacked version of oxView anyway) but might be useful for model generation. The second file is a regular oxDNA file with just the median base pair in each helix (rounded down on the lower indexed strand in the oxDNA file in the case of even-length strands). This also comes with some oxView instructions for generating pretty images overlaying this file on the original mean structure.
