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

Inputs

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Quickstart

Command Line Examples

Clean a PDB file

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• CLI argument: --pdb-file input.pdb

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

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 input_file.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