My Project
Documentation for the PyRosetta Toolkit GUI
Jared Adolf-Bryfogle


Last edited April 2013. Code by Jared Adolf-Bryfogle <>. The PI for this application is Roland Dunbrack <>

Code and Demo

The application is available in both rosetta_source/GUIs/pyrosetta_toolkit and in the newest PyRosetta binary releases.

PyRosetta Setup:

Optional PyMOL Integration Setup:

Optional SCWRL Integration Setup:

Run the program:


Jared Adolf-Bryfogle and Roland Dunbrack (2013) "The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite. " PloS-ONE RosettaCON2012 special collection (Submitted)


This GUI is used to setup Rosetta specific filetypes, do interactive modeling using Rosetta as its base, run rosetta protocols, and analyze decoy results.


This application does not run all Rosetta Applications. It does, however, run the most common ones. Although multiprocessing is implemented, full production runs of many rosetta applications usually require a cluster. Always check relevant Rosetta Documentation on RosettaCommons. Options for all protocols can be added through the Option System Manager or through it's protocol-specific UI. Symmetry is not supported at this time.


File Menu

Load a pose through this menu first either from a file or directly from the RCSB. If you have PyMOL setup, it will send the pose to PyMOL after it loads into Rosetta. Loading a pose will open up the PDB Cleaning window by default to prep the PDB for import into Rosetta.

PDB Cleaning Functions:

Main Window

The main window is used to run common protocols, some anlysis, setup decoy output, and finally set a region.

The default region is the whole protein. To specify loops for loop modeling, regions for minimization or residues for repacking, etc. add a region:


Output Options:


Options Menu

Visualization Menu

PyMOL Integration through the PyMOL Mover. A pose can be shown in PyMOL at any time. Regions can be colored, and the PyMOL Observer can be enabled that updates pymol upon structural and energetic changes to the current pose.

Advanced Menu

The Ligand/NCAA/PTM Manager

Design Toolbox

Enable constraints

Insert data into B factor Column

Per Residue control and Analysis

Analysis Movers:

Protocols Menu

Currently Implemented:

High/Low Resolution Docking

High/Low Resolution Loop Modeling (KIC/CCD)

Fixedbb Design (UI)

Floppytail (UI)

Grafting (UI)



PackRotamers (Rosetta)

PackRotamers (SCWRL)


Server Links:

PDBList Menu

A PDBList is simply a list of full paths to PDB files, one on each line. It is used by the GUI to analyze decoys. Methods for making and using a PDBList reside here.

Main Functions:


Bashrc Setup

This is so you do not need to source each time you want to use Toolkit. Takes a few minutes, but worth it. For more information on to what a bash shell is:

To do this:

PyMOL Setup

Setup so that the pymol server runs + listens each time PyMOL is opened.

Changes since last release

This will be the first release