Cap Chain Breaks

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

Description

This floe uses Spruce function OECapTermini to cap chain breaks. The required input is a dataset with an OEDesignUnit.

Titles of required parameters (promoted names)

  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: CapsBuiltDesignUnits
  • 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_CapsBuiltDesignUnits
  • 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 cap builder will remove a water if it clashes with where the cap is built.
    Default: True

Optional parameters (promoted names)

  • Exclude Residues (exclude_residues) type: string: Exclude specific residues from being capped. Format: ‘RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC]’, e.g. ‘ALA:325: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard. Separate multiple with ‘|’ delimiter.