Documentation for the PyRosetta Toolkit GUI
Jared Adolf-Bryfogle (firstname.lastname@example.org)
Last edited 10/1/18. Code by Jared Adolf-Bryfogle < email@example.com >.
The PI for this application is Roland Dunbrack < Roland.Dunbrack@fccc.edu >
The PyRosetta Toolkit has not been ported to PyRosetta-4 unfortunately and is only distributed and comparable with PyRosetta-3.
The application is available in PyRosetta-3 in
Optional PyMOL Integration Setup:
Optional SCWRL Integration Setup:
pyrosetta/apps/pyrosetta_toolkit/SCWRL directory in the respective OS directory.
Run the program:
pyrosetta_toolkitafter running SetPyRosettaEnvironment.sh (creates an alias).
Jared Adolf-Bryfogle and Roland Dunbrack (2013) "The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite. " PloS-ONE RosettaCON2012 special collection
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.
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:
checking that all residues are able to be read by Rosetta
Current Imports:GUI Session, Param PathList, Loop File
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:
! 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.
The Ligand/NCAA/PTM Manager
Insert data into B factor Column
Per Residue control and Analysis
High/Low Resolution Docking
High/Low Resolution Loop Modeling (KIC/CCD)
Fixedbb Design (UI)
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.
This is so you do not need to source SetPyRosettaEnvironment.sh each time you want to use Toolkit. Takes a few minutes, but worth it. For more information on to what a bash shell is: http://superuser.com/questions/49289/what-is-bashrc-file
To do this:
source full/path/to/SetPyRosettaEnvironment.sh(This file is found in the PyRosetta directory)
Setup so that the pymol server runs + listens each time PyMOL is opened.
run full/path/to/PyMOLPyRosettaServer.py(This file is found in the PyRosetta directory)
This will be the first release