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Rosetta Scripts

Requirements

  • Rosetta : Rosetta modelling suite v3.13 onwards. More information here
  • DSSP : sudo apt-get install dssp
  • Scaffold database : See "Data and material availability" statement at the end of the publication to access the different databases.

Install environment

First, create a working environment by using the YML file provided in this folder:

conda env create -f neosurf.yml
conda activate neosurf

Set up global variables

Set up the global variables in the global_vars.py file. Please, specify the following elements:

  • Path to Rosetta
  • Path to DSSP binary file
  • Path to the split lists of your scaffold database (See below)
  • The number of split lists that constitute your scaffold database
  • (Optional) Target and seed chain name (Note: Chains are renumbered that way during the seed refinement step)

Creating a scaffold database

Once you downloaded a scaffold database, create some split files that will distribute the path of these scaffold PDBs in different list. This will allow a parallelization of the scaffold search.

  1. Create a list with absolute path of all your scaffold PDBs.
  2. Run the following command to create some split files: 
    split -l 15 your_final_list.list --additional-suffix .split
ls -v *.split| cat -n | while read n f; do mv -n "$f" "splitfile_$n"; done
  3. Indicate the path to these split files and adapt the total number of split files in the global variables accordingly.

Run a seed refinement

For a seed refinement, please read the relevant README

Run a seed grafting

After seed refinement and selection of seed candidates, please read the relevant README for grafting them onto a scaffold protein.