Per residue scoring

[Anonymous]

Hi all,

I want to be able to get score information for individual residues from my decoys. What is the easiest way to do this currently? I couldn’t find a relevant option in the documentation, do I have to use RosettaScripts or something? I found some old posts on this topic, but I figured I’d ask again in case things have changed in more recent versions.

Thanks!

[Anonymous]

If you have PDB output, the per-residue scores should be listed in tabular format at the end of the PDB. (Just open it up as a text file.) – One caveat is that due to technical issues some of the hydrogen bonding energies are not necessarily broken out into their component columns appropriately. (Although the totals should be correct.)

If that doesn’t work for you, you can use the per_residue_energy and residue_energy_breakdown applications, which can take all the types of input files which Rosetta can read (PDB, silent file, etc.). It also breaks out the hydrogen bonding terms appropriately.

https://www.rosettacommons.org/docs/latest/application_documentation/analysis/residue-energy-breakdown

residue_energy_breakdown split things out based on pairs of residues. (e.g. you can see the energy of ASP115 interacting with LYS212). If you want residue-level summaries like in the PDB table, you can use the per_residue_energy application instead.

[Anonymous]

Hi rmoretti,

Thanks as always for your reply. To clarify, is it necessary to specify PDBoutput during production , or can I call it when scoring a silent file? Since I usually output silent files, I’m attracted to residue_energy_breakdown.linuxgccrelease. However, I can’t seem to find it in my installation of Rosetta-3.5! Do you know why that might be or how I could get that executable?

[Anonymous]

The per_residue_energy and residue_energy_breakdown applications should be able to handle silent file input.

Those applications aren’t in Rosetta3.5, though. You would need to get one of the weekly releases in order to have it. (Although if compatibility with Rosetta 3.5 is an absolute must, I might be able to dig up an older version which would be compatible.)

[Author]

Posts