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calculate RMSD (RNA modelling)

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calculate RMSD (RNA modelling)


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

Best Regards


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Tue, 2016-07-05 01:58

The score and probably score_jd2 applications have tools for calculating RMSD to natives after a run.

Tue, 2016-07-05 07:11


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

Tue, 2016-07-12 02:40

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


Tue, 2016-07-12 05:49

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>


Tue, 2016-07-12 09:32


Thank you for your help. It worked fine!

Wed, 2016-07-13 09:11