With RNA modelling in Rosetta, how may i get the RMSD to a native structure for the whole set of generated models? I forgot to run the rna_denovo.linuxgccrelease with the -native flag and now, i would like to measure the RMSD for the obtained models (.out file) agaisnt the crystallographic structure.
Thanks a lot in advance
The score and probably score_jd2 applications have tools for calculating RMSD to natives after a run.
Thank you for the reply. I tried with:
score_jd2.linuxgccrelease -in:file:native 4pdb_RNA.pdb -in:file:silent 38NT_APT.out
but the problem is that this is an aptamer (RNA) and not a protein, so apparently it does not calculate the RMSD (set to 0 in all cases).
Any further insights? I could not find a command under RNA_tools
Thanks a lot
The problem is probably that the RMSD tools default to Calpha RMSDs. I'll ask Rhiju if he's already got a tool for this, but in the meantime, probably your next best bet is pyrosetta, or something on https://www.rosettacommons.org/docs/latest/application_documentation/rna/rna-applications.
Rhiju says rna_score will do this.
rna_score -just_calc_rmsd -in:file:silent <input file > -out:file:silent <output file> -native <native PDB>
Thank you for your help. It worked fine!