The M2-seq analysis was conducted using the commands in m2seq.m which use the scripte run_m2seq_plots.m. 1D reacitivity data can be found in m2seq/.
All command used for modeling, auto-DRRAFTER and ERRASER2 can be found in autodrrafter_commands.txt, with the inputs found in models/modeling_inputs/.
Convergence was calculated using the command below, and tabulated in convergence/.
drrafter_error_estimation.default.linuxgccrelease -s *.pdb -mute core -rmsd_nosuper true --per_residue_convergence true | awk '{print $NF}'
Stereochemical and map-fit validation metrics were calculated using the https://github.com/DasLab/CASP15_RNA_EM, example scripts are get_scores_singleconf.py and get_scores_multiconf.py. Results can be found in map_to_model/.
Inter-helical and hinge angles were calculated in pymol using the commands angle_scripts.txt which use the script get_all_angles.py.
FSC-curves were prepared with convert_all_fsc.sh using the script fsc_cs2_to_emdbxml.sh.
For descriptions of secondary structure across the coronavirus SL5s get_secstruct_info.py was used.