Included in this directory is a set of example structures and tutorials to help you get started. Structures used in our paper are also included to help you reproduce them.
Following the protocols in our upcoming paper, the following directories contain structures and instructions for each of the examples
- Importing multiple components from CaDNAno
- Freeform design of a tetrahedron
- Is a continuation of 2. demonstrating RBD and oxServe dynamics
- An example of extending oxDNA Analysis Tools
- Two scripting examples
5a. Two examples of using scripting to edit a structure
5b. Building a nanocrystal with scripting - Is a general protocol for creating ANM models
- Building a tetrahedral protein cage
Examples reproducing the analysis figures of our paper can be found in the oxdna_analysis_tools repository. The structures are as follows:
- Holliday junction
- Design 20
- Design 23.
- RNA tile trajectory
- TMF open
- TMF closed
- H-bonds RNA Tile
- RNA rectangle
As described earlier, caDNAno files exported to oxDNA using conversion tools will be planar and near impossible to relax using the usual relaxation methods in oxDNA. The following examples showcases our rigid-body simulator that attempts to automatically rearrange these flat CaDNAno designs to a configuration that can be relaxed using traditional molecular dynamics methods.
1. Rigid-body triangle This is a minimal example of a triangle (well, technically a circle) drawn as three parallel helices in caDNAno. Clustering and applying rigid-body dynamics rearanges the helices into a triangular shape.
2. Rigid-body square This is a larger example where a connected set of four 6-helix bundles are converted from caDNAno, clustered and then automatically relaxed into a square.