The Design API runs the rosetta Rosetta FastDesign protocol (https://github.com/CyrusBiotechnology/design-workflow/blob/master/workflow-environment/fastdesign.xml ) given an input PDB file and a resfile. given an input PDB file and a residue file (resfile). FastDesign performs FastRelax with design enabled to create designed structures for residue parameters defined by the input resfile (See References for more information on the FastDesign protocol)

Quickstart

Run design on an input structure to generate 10 new design models

cyrus engine submit design --pdb-file=input.pdb --res-file=input.res --repeats 10

Inputs

• --pdb-file

  • Input PDB file to run design on

  • The PDB file should be cleaned prior to input using the Clean PDB API.

...

• --res-file

  • Input residue file

  • The resfile is a standard Rosetta

...

• • resfile, documented here: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles

The API is used as follows:

...

Options

• --repeats

...

• (int32)

  • Number of iterations to relax

  • default = 1

Output

• models.tgz

  • Designed models

References

Rosetta FastDesign

Rosetta Resfile