Radius Of Gyration API

The Radius Of Gyration API provides an interface to score a protein structure in Rosetta using the Radius of Gyration score term. This is frequently used to filter backbones generated by RF Diffusion, in particular to filter out backbones that are nothing but long extended helices.

Command Line Interface

Examples

Score one PDB using radius-of-gyration

lev engine submit radius-of-gyration input.pdb

Score multiple PDBs in a batch submission

# All PDB files in the current directory using wildcard
lev engine submit radius-of-gyration *.pdb

# All PDB files compressed and zipped into a tarball
lev engine submit radius-of-gyration input.tgz

The input *.pdb will access all files ending in .pdb in the current directory. input.tgz is a compressed and zipped collection of PDB files. For instructions on how to generate input.tgz, see How to create a tgz file for batch inputs.

Flags

  • --batch-size (int) (Default: 100)
    • The number of PDB files to process in each batch. This should not need to be changed unless you are looking to run 10s of thousands of inputs. In which case it’s recommended to discuss with support first.
  • --chain (str) (Optional)
    • Select the chain you wish to perform scoring on. Leave blank to use all chains.
  • --pdb-file (str) (Required)
    • The path to a PDB file or files containing the protein backbone you want to score.
    • Example:
      • --pdb-file input.pdb --pdb-file input2.pdb
      • --pdb-file *.pdb
      • --pdb-file input.tgz

Python Interface

Examples

Score one PDB using radius-of-gyration

from engine import EngineClient

client = EngineClient()
client.authorize()

job_id = client.submit_radius_of_gyration(
    pdb_path="input.pdb"
)

Flags

  • batch_size (int) (Default: 100)
    • The number of PDB files to process in each batch
  • chain (str) (Optional)
    • Select the chain you wish to perform scoring on. Leave blank to use all chains.
  • pdb_paths (List[str]) (Required)
    • The path to a PDB file or files containing the protein backbone you want to score.
    • Example:
      • ["input.pdb", "input2.pdb"]

Outputs

  • score.sc (rosetta scorefile)
    • A score file containing the radius of gyration score for your structure or structures.

Updated: