Use manual rigid-body transformation to prepare the initial conf. of multi-component json file
Use oxDNA's converter to create the topology and the configuation files.
Open cadnano, specify the staple colors as different groups and save as another json file
Move MATLAB directory to the folder and run RBT_Conf.m. Follow the instructions to select the topology, configuration and the json file. Note the json files for importing doesn't hvave to be the same. One can break the staples into several pieces with different colors. The staple colors simply are used as seeds for categorization.
Details in: Huang, C. M., Kucinic, A., Le, J. V., Castro, C. E., & Su, H. J. (2019). Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis. Nanoscale, 11(4), 1647-1660.