Author

Jared Adolf-Bryfogle

Metadata

This document was last updated December 2012, by Jared Adolf-Bryfogle jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com. The PI for this application is Roland Dunbrack Rolan.nosp@m.d.Du.nosp@m.nbrac.nosp@m.k@fc.nosp@m.cc.ed.nosp@m.u

The application was developed by:

• Jared Adolf-Bryfogle

Code and Demo

The Code is available in rosetta_source/GUIs/pyrosetta_toolkit. Use ./pyrosetta_toolkit.py within the code directory to run the application.

References

Reference in Publication.

New_Library contains code for this purpose

This GUI is used to run Rosetta protocols, setup Rosetta specific filetypes, and analyze PDB files and Rosetta decoy outputs.

Limitations This application does not run all Rosetta Applications. It does, however, run some of the most common ones. Although multiprocessing is implemented, full production runs of rosetta applications usually require a cluster. Always check relevant Rosetta Documentation on RosettaCommons. Additional options for most protocols can be added through the Option System Manager.

Modes

Main Window

File Menu

Advanced Menu

Protocol Menu

PDBList Menu

Help Menu

Input Files

PDB, PDBList If there are any special input file types, describe them here.

• Common file types (loop file, fragment files, etc) will be described in a common place; link to those documents with the ATref command.
• Uncommon and app-specific file types should be described here.
• Link to (or at least give paths to) examples of each from your integration test/demo.
• Mention what you expect the input structure to be: if it's loop modeling, does the loop need to be present, or will it build from scratch? If it's ligand binding, does there need to be a copy of the ligand in the input structure?

Tips

-Setup PyRosetta in BashRC. -Use PyMOL Integration - Setup auto server -Set default Options -Set default Scorefunction -Advanced Users: To add windows and functions to the GUI see supplemental material in the paper.

Expected Outputs

-List outputs available What does your protocol produce? Usually it will be just a PDB and a scorefile, but note if there should be more. Note what the normal exit status of the protocol is (for example, "You'll see the jd2 x jobs completed in y seconds message if successfully completed".)

Post Processing

? talk about PDBList? What post processing steps are typical? Are score vs RMSD plots useful? Are structures clustered (if so, give a command line)? Is it obvious when either the application has succeeded or if it has failed (e.g. if the protocol makes predictions like "This is the docked conformation of proteins A and B"). In the case of designs, how should designs be selected?