The Clean PDB API prepares input PDB files for optimal performance using the Cyrus Engine APIs. When a PDB file is submitted to the API the following changes are made:

• All waters are removed

• All metal ions are removed

• All small molecule ligands are removed

• All non-canonical amino acids are converted to the most similar canonical amino acid

• Residues are renumbered starting from 1

Cyrus recommends that all PDBs used with the Cyrus Engine API are first passed through this endpoint. prior to use.

Quickstart

Command Line Examples

Clean a PDB file:

cyrus engine submit clean-pdb input_file.pdb

Clean a PDB from RCSB for chains A and B

cyrus engine submit clean-pdb --pdb-id 3hmx --chains A,B

Python Examples

Clean a PDB file:

from engine.clean_pdb.client import CleanPdbClient

client = CleanPdbClient()
job_id = client.submit(pdb_path="input.pdb")

Inputs

Either a PDB file or a published PDB ID (ex. 1ubq)

Options

• --pdb-file

  • Input PDB file

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

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

• --pdb-id

  • PDB ID to download from RCSB (if not providing input PDB)

• --chains

  • Comma separated list

  • List of chain IDs to include in output, or all to download all chains

  • default = all

Outputs

• full_structure.pdb -- A cleaned PDB file