Summary of examples:

Examples using the tRNA crystal structure 6TNA to demonstrate various coarse-graining schemes:
    Example 1: 6TNA with only C3' atoms
    Example 2: 6TNA with only P atoms
    Example 3: 6TNA with P and C3' atoms
    Example 4: 6TNA with P, C2 and C3' atoms

Examples using other ideal coarse grain templates (all C3' representations):
    Example 5: Yeast ai5g group II intron using the 1KXK crystal structure
    Example 6: Aminoacyl-tRNA synthetase ribozyme (flexizyme) using the 3CUL crystal structure
    Example 7: P4-P6 using the 1GID crystal structure
    Example 8: Azoarcus group I intron using the 1ZZN crystal structure with loops added by NAST
    Example 9: Twort ribozyme using the 1Y0Q crystal stucture with loops added by NAST

Examples using NAST coarse-grain models of tRNA (all C3' representations):
    Example 10: Class A model (additional NAST models used in the paper are in the data folder)

Examples for parsing .bpseq format files to get the -FD.txt fragment definition file:
    BPSEQexample