Discrepancy between the total pose energy and sum of per residue energies

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    • July 2, 2013 at 2:24 pm #1631
      Anonymous

        Hi all

        I tried summing up all the per residue energies reported by Rosetta 3.4, and figured out that the sum of the per residue energies dosent match with the total pose energy reported at the end of the annotated PDB file. Could any any explain the discrepancy or am i missing out some thing.

        Secondly, going through the Rosetta 3.4 documentation, i came across the “residue_energy_breakdown” utility. Unfortunately, i was not able to find any executable by name “residue_energy_breakdown.linuxgccrelease” under rosetta3.4/rosetta_source/bin. Could any one let me know if any related utility does exists in Rosetta.

        Thanking in advance

        R.Vijayan

      • July 2, 2013 at 2:37 pm #8985
        Anonymous

          Hi, this is due to the hydrogen bond energies. See this post:

          https://www.rosettacommons.org/content/rosetta-scoring

          If you need the hbond energies, the only way I know to access them is through PyRosetta: https://www.rosettacommons.org/node/3287
          Someone else may know a way to have them printed through an application.

        • July 2, 2013 at 3:43 pm #8986
          Anonymous

            Thanks

            R.Vijayan

          • July 2, 2013 at 6:43 pm #8988
            Anonymous

              The residue_energy_breakdown application is an unreleased pilot app, so it doesn’t show up in the compiled release.

              The released but undocumented ScoreCutoffFilter from RosettaScripts does similar functionality, though.

              <ScoreCutoffFilter name="scofilter" report_residue_pair_energies=1 cutoff=5000.0 >

              The report_residue_pair_energies=1 will cause the filter to output a residue pair energies to the tracer at the end of the run. (Technical detail – you’ll need to score the pose first, either with ScoreMover, or some other mover which applies a scorefunction to the pose.)

              Regarding getting hydrogen bonding breakdowns, there unfortunately isn’t an external flag to do this – you either need to handle it programatically (e.g. through PyRosetta), or use an application which does it for you. I don’t know if ScoreCutoffFilter does this, though residue_energy_breakdown does. (If you really need it, you can email me [click the envelope to the left] and I can forward you a pre-release copy of the residue_energy_breakdown application.)

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