Page Comparison

...

• --pdb-file (str)

  • Input PDB file – a cleaned and/or relaxed PDB file

  • Prepare a clean PDB using the Clean PDB API

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

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

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

  • Cyrus strongly recommends using the Prepare or Relax tool in Cyrus Bench to preprocess models before uploading to this API.  This will number your models as expected and provide a more stable scoring baseline and will make interpreting results easier.

• --disulfide-list (str)

  • A list of residue number pairs which should form disulfide bonds

    • pairs annotated using “:”, multiple pairs are comma delimited

  • CLI argument: --disulfide-list “1:10,3:5”

  • Python submit() argument: disulfide_list=[(1,10), (3,5)]

  • Each residue should only be referenced in one disulfide pair

  • Residues in the disulfide list should not already be in disulfides (this will result in an error)

...