Getting Started

Build Documentation

Rosetta Tutorials

Rosetta Basics

Rosetta Applications

Rosetta Scripting Interfaces

Development Documentation

Internal Documentation

How to Write Documentation

FAQ

Glossary

RosettaEncyclopedia

Options list

Page history

CustomBaseTypePackerPalette documentation created by Vikram K. Mulligan (vmulligan@flatironinstitute.org) on 20 February 2019.

Description

A PackerPalette permitting design with the canonical 20 amino acids plus a user-specified list of other base types.

RosettaScripts Details

Autogenerated Tag Syntax Documentation:

Sets up a packer palette that expands the default (canonical) residue type set with user-defined base types or types selected by ResidueProperties.

References and author information for the CustomBaseTypePackerPalette packer palette:

CustomBaseTypePackerPalette PackerPalette's citation(s): Mulligan VK, Kang CS, Sawaya MR, Rettie S, Li X, Antselovich I, Craven T, Watkins A, Labonte JW, DiMaio F, Yeates TO, and Baker D. (2020). Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Sci 29(12):2433-45. doi: 10.1002/pro.3974.

<CustomBaseTypePackerPalette name="(&string;)"
        additional_residue_types="(&string_cslist;)" />
  • additional_residue_types: A comma-separated list of additional residue types (by full base name) to add to the PackerPalette.

Example

The following example creates a palette that allows both L- and D-amino acids (and GLY), then uses the Phi ResidueSelector to restrict design to L-amino acids at positions in the negative-phi region of Ramachandran space, and to D-amino acids at positions in the positive-phi region of Ramachandran space:

<ROSETTASCRIPTS>
    <SCOREFXNS>
        <ScoreFunction name="r15" weights="ref2015.wts"/>
    </SCOREFXNS>
    <PACKER_PALETTES>
        <CustomBaseTypePackerPalette name="palette" additional_residue_types="DALA,DCYS,DASP,DGLU,DPHE,DHIS,DILE,DLYS,DLEU,DMET,DASN,DPRO,DGLN,DARG,DSER,DTHR,DVAL,DTRP,DTYR" />
    </PACKER_PALETTES>
    <RESIDUE_SELECTORS>
        <Phi name="posPhi" select_positive_phi="true" ignore_unconnected_upper="false" />
        <Not name="negPhi" selector="select_positive_phi" />
    </RESIDUE_SELECTORS>
    <TASKOPERATIONS>
          <ReadResfile name="l_res" filename="inputs/l_res.txt" selector="negPhi"/>
          <ReadResfile name="d_res" filename="inputs/d_res.txt" selector="posPhi"/>
    </TASKOPERATIONS>
    <MOVERS>
        <PackRotamersMover name="packer" scorefxn="r15" task_operations="l_res,d_res" packer_palette="palette" />
    </MOVERS>
    <PROTOCOLS>
        <Add mover="terminal_bond1"/>
        <Add mover="terminal_bond2"/>
        <Add mover="packer"/>
    </PROTOCOLS>
    <OUTPUT scorefxn="r15" />
</ROSETTASCRIPTS>

The resfile l_res.txt would look like this:

PIKAA ACDEFHIKLMNPQRSTVWY
start

And the resfile d_res.txt would look like this:

PIKAA X[DALA]X[DCYS]X[DASP]X[DGLU]X[DPHE]X[DHIS]X[DILE]X[DLYS]X[DLEU]X[DMET]X[DASN]X[DPRO]X[DGLN]X[DARG]X[DSER]X[DTHR]X[DVAL]X[DTRP]X[DTYR]

See also