Member Site › Forums › ROSIE › ROSIE – General › A table of residue-residue pair energies for residues which interact across the docking interface missing in output
- This topic has 4 replies, 2 voices, and was last updated 11 years, 6 months ago by Anonymous.
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April 22, 2013 at 9:47 pm #1564Anonymous
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? -
April 22, 2013 at 9:55 pm #8662Anonymous
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.
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April 23, 2013 at 6:47 pm #8671Anonymous
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. -
April 26, 2013 at 9:34 pm #8684Anonymous
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
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May 3, 2013 at 8:02 pm #8717Anonymous
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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