Basic DNA Origami Tutorial
This tutorial walks through the process of creating a simple DNA origami structure using mrDNA.
Loading a design from cadnano
from mrdna.readers import read_cadnano
# Load a cadnano design
model = read_cadnano('6hb.json')
Visualizing the structure
You can generate PDB files to visualize the structure in molecular viewers like VMD or PyMOL:
# Create a coarse-grained model
model.generate_bead_model(max_basepairs_per_bead=5, max_nucleotides_per_bead=5)
# Output PDB files
model.write_pdb('6hb_cg.pdb')
Running a simulation
from mrdna.simulate import multiresolution_simulation
# Run a multi-resolution simulation
result_dir = multiresolution_simulation(
model,
output_name='6hb',
gpu=0,
coarse_steps=5e7,
fine_steps=5e7
)