calculate RMSD (RNA modelling)

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    • July 5, 2016 at 8:58 am #2460
      Anonymous

        Dears

        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

        Obdulia

      • July 5, 2016 at 2:11 pm #11717
        Anonymous

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

          https://www.rosettacommons.org/docs/latest/application_documentation/analysis/score-commands

        • July 12, 2016 at 9:40 am #11723
          Anonymous

            Hi,

            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

          • July 13, 2016 at 4:11 pm #11741
            Anonymous

              Dears,

              Thank you for your help. It worked fine!

            • July 12, 2016 at 12:49 pm #11724
              Anonymous

                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.

                 

              • July 12, 2016 at 4:32 pm #11737
                Anonymous

                  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>

                   

                   

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