Relax

The Relax API runs the Rosetta FastRelax protocol. This is useful for taking a structure not generated by Rosetta and “relaxing” it into the Rosetta scorefunction preparatory to further modeling, or for generating a backbone ensemble for a further modeling experiment.

 

Quickstart

Command Line Examples

Create 10 new relaxed models of input.pdb:

cyrus engine submit relax input.pdb --repeats 10

Python Examples

Create 10 new relaxed models of input.pdb:

from engine.relax.client import RelaxClient client = RelaxClient() job_id = client.submit(pdb_path="input.pdb", repeats=10)

Inputs

  • --pdb-file

    • Input PDB file

    • CLI argument: --pdb-file input.pdb

    • Python submit() argument: pdb-file=”input.pdb”

    • Do not include nonprotein residues.

    • Do not include multimodel (NMR-sourced) PDBs.  

Options

  • --repeats

    • The number of different relaxed conformations the loop modeling API will return.

    • CLI argument: --repeats 5

    • Python submit() argument: repeats=5

    • default = 1

Outputs

  • models (directory)

    • PDB files with relaxed structures.  The models will be in the form input_####.pdb, where #### is an index (0001, increasing).  

    • Note that Rosetta will renumber the residues monotonically starting from 1, contiguous across chains.

  • score.sc

    • A text file containing the Rosetta scores for each generated model.

Notes

Rosetta FastRelax

Quoting from the RosettaCommons documentation:

“This finds low-energy backbone and side-chain conformations near a starting conformations by performing many rounds of packing and minimizing, with the repulsive weight in the scoring function gradually increased from a very low value to the normal value from one round to the next.” 

Output File interpretation

Results can be downloaded if and only if a job has succeeded – DONE state

Model quality can be assessed via scores.  Broad documentation on interpreting scores can be found here.  The score.sc file is a space-delimited data table, padded for easier reading.  It can be parsed with pandas dataframes, excel, or your tool of choice.  In the score.sc file, pay particular attention to the total_score column.  The total_score is Rosetta’s overall grade for a model.  The total_score should have a negative value for good models, although this will depend enormously on the quality of the input model. 

Usually you should sort your models by total_score, look at the lowest-scoring 5 or so, pick the one your biophysical intuition says is best, and proceed with it for whatever your further experiment is.