doDesign

Quick script for running fixed backbone design using PyRosetta

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

This script requires the user to have a license and copy of PyRosetta version 4. Licensing is free for academic and non-profit institutions and is available to commercial users for a fee. Please see PyRosetta for more details.

How to use

Simply download and run doDesign.py in your terminal. There are several command-line arguments that doDesign.py takes. You can find more details about those by executing

/usr/bin/python doDesign.py -h

which will yield the following description:

usage: doDesign.py [-h] [-f input.pdb] [-res RESFILE] [-o output] [-j JOBS]
                   [--pymol] [-sfxn SFXN]

optional arguments:
  -h, --help    show this help message and exit
  -f input.pdb  input PDB file for design
  -res RESFILE  resfile to use for design
  -o output     output file stem (don't include the .pdb)
  -j JOBS       number of times to perform design (default: 1)
  --pymol       Outputs structures to PyMOL instance (default: False)
  -sfxn SFXN    ScoreFunction to use for design (default: ref2015)

For more info on how to create resfiles please see the Rosetta Documentation. To use the PyMOL output, you must also run the script PyMOL-RosettaServer.py (included with PyRosetta) within an instance of PyMOL before running this script.

run PyMOL-RosettaServer.py

If not supplied, the options will be set to their default values. Options without a default value are mandatory.

Example

Let's take, for example, the Trp-cage protein (pdb code 1L2Y) and save it as 1L2Y.pdb

We want to redesign every residue of the protein to allow substitution with any other amino acid. To do this, create a resfile 1L2Y.res with the following content:

ALLAA
start

If we want to generate 300 structures and monitor our output in PyMOL we could use doDesign as follows:

/usr/bin/python doDesign.py -f 1L2Y.pdb -res 1L2Y.res -o 1L2Y_out -j 300 --pymol

Our PyMOL instance should now be displaying our new structures and they should be output as pdb files with the name 1L2Y_out_n.pdb where n is a number corresponding to which of the 300 structures it is.

An additional file, 1L2Y_out.fasc will be generated, summarizing the energy of each design.

Authors

• Benjamin Walcott - walcob

Acknowledgments

• RosettaCommons