A table of residue-residue pair energies for residues which interact across the docking interface missing in output

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    • #1564
      Anonymous

        I cannot find the table of residue-residue pair energies for residues which interact across the docking interface in any of the output of the server including the stats at the lower listing in the model pdb files.
        Could someone tell me if I have missed this output or how to request this output from the server?

      • #8662
        Anonymous

          Can you point me to the documentation / paper that suggests the output should be there? I’m not aware of any code in Rosetta that does this. It can certainly BE done, but I don’t know of anyplace that it IS done.

        • #8671
          Anonymous

            Yes from the website under the support page on analysis is an example:

            A table of residue-residue pair energies for residues which interact across the docking interface. Energies are defined the same as in previous tables.
            example:
            Pair energies across interface
            res1 aa1 res2 aa2 total Eatr Erep Esol Ehbnd Epair Egb Ecst Eplane Eh2o Eh2o_hb
            B 19 PHE C 812 ARG -0.56 -1.18 0.17 0.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00
            B 28 THR C 808 ARG 0.05 -0.01 0.00 0.05 0.00 0.01 0.00 0.00 0.00 0.00 0.00
            B 28 THR C 812 ARG 0.01 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00
            B 30 LYS C 800 TRP 0.04 -0.03 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00
            B 30 LYS C 801 ARG 0.04 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.00
            B 30 LYS C 805 VAL -0.51 -0.58 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00
            B 30 LYS C 808 ARG -0.04 -0.12 0.00 0.05 0.00 0.04 0.00 0.00 0.00 0.00 0.00
            B 30 LYS C 809 TYR -0.08 -0.55 0.77 0.74 -1.04 0.00 0.00 0.00 0.00 0.00 0.00
            A table of starting minus finishing χ angles, and absolute χ angles. These can be helpful to detect residues which change rotameric state upon docking. The fraction of residues with unchanged rotamers is also reported.

          • #8684
            Anonymous

              You are right that those scores aren’t present in the PDBs as the documentation states – I’ve filed a bug report and will see what we can do to fix it. https://carbon.structbio.vanderbilt.edu/mantisbt/view.php?id=257

            • #8717
              Anonymous

                It turns out the documentation was copied from old Rosetta++ documentation. Nobody has ever ported the code that made those calculations to Rosetta 3. (I assume this means none of us found it particularly useful). I’ve filed a feature request to return those reports to circulation, but it will be a long while before anyone does it.

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