Residue State Changer

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 OEBio function OESwapAIEResidueAtoms and Spruce function OEProtonateDesignUnit to flip and change the ionization state of specific residues in a design unit. The required input is a dataset with an OEDesignUnit.

Titles of required parameters (promoted names)

  • Failure Dataset (data_out) type: dataset_out: Dataset with design unit that failed to be successfully modelled.
    Default: failed_ResidueStatesModifiedDesignUnits
  • Input Design Unit (data_in) type: data_source: Dataset with design unit(s) to be modelled
  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: ResidueStatesModifiedDesignUnits
  • Residue to edit (residue) type: string: Select residue to edit. 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.

Optional parameters (promoted names)

  • Flip residue (flip) type: boolean: Flip ambiguous isoelectronic residue atoms
    Default: False
  • Change protonation state of residue (prot_state) type: boolean: Change protonation state of residue, protonate or de-protonate.
    Default: False
  • Re-optimize hydrogen bonding network (reoptimize) type: boolean: Re-optimize hydrogen bonding network after state changes
    Default: True
  • Switch hydrogen atoms on His residue(s) (switch) type: boolean: Switches the hydrogens on histidine residue atoms (HID/HIE)
    Default: False