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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
)