Build Sidechains

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/SPRUCE

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Structural Data Preparation

  • Task-based/Target Prep & Analysis/Protein Preparation


This floe uses Spruce function OEBuildSidechains to build partial amino acid residues. The required input is a dataset with an OEDesignUnit.

Titles of required parameters (promoted names)

  • Input Design Unit (data_in) type: data_source: Dataset with design unit(s) to be modelled
  • Failure Dataset (data_out) type: dataset_out: Dataset with design unit that failed to be successfully modelled.
    Default: failed_PartialSidechainsBuiltDesingUnits
  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: PartialSidechainsBuiltDesingUnits
  • Add hydrogens to DU (switch) type: boolean: If off, then the DU will not be (re-)protonated. If on, then missing hydrogens are protonated and partial charges will be recomputed.
    Default: True
  • Delete Clashing Solvent (del_solvent) type: boolean: The sidechain builder will remove a water if it clashes with built piece.
    Default: True
  • Rotamer Coverage (rot_coverage) type: decimal: Limits the number of rotamers checked for each residue type, based on frequency.
    Default: 100.0
  • Rotamer Library (rot_lib) type: string: Rotamer library to use for side-chain building.
    Default: Richardson2016
    Choices: Dunbrack, Richardson, Richardson2016

Optional parameters (promoted names)

  • Build Residues (build_residues) type: string: Build these specific residues (format is RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC] - separate multiple with | delimiter.