Rosetta-scripts comprises a set of helper scripts for homology and de novo modeling with Rosetta. A tutorial to get started with Rosetta and rosettascripts is available here Currently rosettascripts contains the following Python and Unix utilities:

• submitJobs: running multiple Rosetta jobs in parallel using a rna_denovo master file

  Usage

  submitJobs -i <FARFAR input script> [-d <directory>] [-p <number of processors>]
  

• extract_pdb: extract decoys from a Rosetta silentfile and optionally concatenate them into a single multi-model PDB file

  Usage

  extract_pdb -s <silentfile> -f <folder with silentfiles> -n <number of models> -e <extract pdbs (true|false, default: true)> -m <merge pdbs (true|false, default: false)>
  

• pdb_resi_renumber: renumber the residues of a PDB file

  Usage

  pdb_resi_renumber [-h] [--version] -pdb PDB [-i] -e EDIT [-o O]
  
  renumber residues in PDB files
  
  optional arguments:
    -h, --help            show this help message and exit
    --version             show program's version number and exit
    -pdb PDB              pdb input file (.pdb)
    -i                    in-place modification
    -e EDIT, --edit EDIT  'oldResi>newResi' (use "," to separate individual residues and "-" for residue ranges; e.g. '2-4,5>A:6-8,9')
    -o O                  pdb output filename
  

• process_silentfile: remove non-standard residues from a silentfile

  Usage

  process_silentfile -s <silentfile>
  

Tutorial on riboswitch de novo modeling

We outline the steps involved in setting up a de novo modeling pipeline using Rosetta's FARFAR2 protocol (Watkins et al., Structure 2020). Here, we demonstrate the workflow by modeling a manganese riboswitch.