Rotamers of a Residue

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 OERotamers to generate and return design units with different rotamers of a protein residue. The required input is a dataset with an OEDesignUnit.

Parameter title in user interface (promoted name)

  • Failure Dataset (data_out) type: dataset_out: Dataset with design unit that failed to be successfully modelled.
    Default: failed_RotamerSpinDesignUnits

Parameter title in user interface (promoted name)

  • Input Design Unit (data_in) type: data_source: Dataset with design unit(s) to be modelled

Parameter title in user interface (promoted name)

  • Remove clashing rotamers (remove_clashing) type: boolean: Remove rotamers that clash with the remaining atoms.
    Default: True

Parameter title in user interface (promoted name)

  • Residue Chain ID (res_cid) type: string: Chain ID of residue to get rotamers for.

Parameter title in user interface (promoted name)

  • Residue Insertion Code (res_ins) type: string: Insertion code of residue to get rotamers for.
    Default: :blue:` `

Parameter title in user interface (promoted name)

  • Residue Name (res_name) type: string: Name of residue to get rotamers for.

Parameter title in user interface (promoted name)

  • Residue Number (res_num) type: integer: Number of residue to get rotamers for.

Parameter title in user interface (promoted name)

  • Rotamer Coverage % (rot_coverage) type: decimal: Coverage of the rotamers returned from the library in percent.
    Default: 100.0

Parameter title in user interface (promoted name)

  • Rotamer Library (rot_lib) type: string: Rotamer library to use for side-chain building.
    Default: Richardson2016
    Choices: Dunbrack, Richardson, Richardson2016

Parameter title in user interface (promoted name)

  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: RotamerSpinDesignUnits