Several Python scripts were written by developers and users to help others use PyRosetta. You are also encouraged to examine the code for the test scripts found in the /test folder of your PyRosetta install directory.

PyMOL Scripts

PyMOL is the favorite visualizer to use among the PyRosetta community — so much so that we built a Mover specifically for sending structures directly to an instance of PyMOL running the "listener" script.

PyMOL Servers ("Listeners")

PyMOL must run a "listener" script to properly translate packets sent to it from PyRosetta. These listeners can only translate a few types of packets but can be customized to translate any desired output. If you plan on using PyRosetta with PyMOL often, we recommend you add the line run to your .pymolrc file so that PyMOL starts up automatically listening to PyRosetta. The script is found in your PyRosetta install directory. For more details, please see the PyMOL_Mover Tutorial.

Sample Scripts

A collection of sample/demo scripts found in the /demos folder are outlined here. The demo scripts demonstrate PyRosetta's data structures, syntax, and traditional applications. Any data files required by default are also provided in the /test/data or /demos/data directories. Since these sample scripts are filled with comments on usage, we've also provided a summary of the terms and format used.

Essential Objects

Folding Applications

Docking Applications

Protein Docking

DNA Docking

Small Molecule Docking


Numerous helper scripts have been developed to make using PyRosetta easier. We provide a sampling of tools below, which can also be found in the /toolbox folder.

Several of the Tools below rely on third-party software. If using PyRosetta on a computer network, make sure to obtain or request the required software. These tool scripts are meant to provide a starting point for many custom applications.

Unfortunately, the rapid changes to Rosetta and PyRosetta have made support difficult. The tools provided here are developer favorites or use methods essential to some PyRosetta applications. These may not work with all versions of PyRosetta and have only been tested with PyRosetta v2.0 beta or intermediate revisions, unlike the sample/demo scripts, which are tested with every new build. Once you are experienced using Python and PyRosetta (by performing the workshops and studying the sample scripts), editing these files to your liking should be fairly easy.

Current Tools