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
Description
This floe uses Spruce function OEBuildSidechains to build partial amino acid residues. 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_PartialSidechainsBuiltDesingUnits
Parameter title in user interface (promoted name)
Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.Default: PartialSidechainsBuiltDesingUnits
Parameter title in user interface (promoted name)
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
Parameter title in user interface (promoted name)
Delete Clashing Solvent (del_solvent) type: boolean: The sidechain builder will remove a water if it clashes with built piece.Default: True
Parameter title in user interface (promoted name)
Rotamer Coverage (rot_coverage) type: decimal: Limits the number of rotamers checked for each residue type, based on frequency.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: Richardson2016Choices: Dunbrack, Richardson, Richardson2016
Parameter title in user interface (promoted name)
Input Design Unit (data_in) type: data_source: Dataset with design unit(s) to be modelled