Author

Jared Adolf-Bryfogle

Metadata

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/RosettaFlagBuilder To run the GUI use ./RosettaFlagBuilder.py in the code directory.

The DoxygenParser class is available in rosetta_source/GUIs/pyrosetta_toolkit/modules

References

Refs in Publication

New_Library contains code for this purpose

The purpose of this GUI is to help running, exploring, and building flag files for Rosetta applications. It is useful for exploring both documentation and available options and default settings of the many Rosetta applications.

Algorithm

This GUI parses Rosetta Doxygen documentation and the -help flag for each application.

Limitations

This application attempts to help in formatting a Rosetta flag file and exploring documentation. However, numerous applications have special formatting for Doxygen documention, including embeded HTML. Efforts are under way to standardize and better parse the formatting, but please refer to rosettacommons for full production runs.

Modes

Main Window

Path Builder

Qsub Cluster Setup GUI

Input Files

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

To get all available options given to a particular app, choose Repopulate->x This overwhelms the Tk GUI, but can be useful if you want to go off the beaten path. For an individual app that is selected, you can click x. QsubClusterSetup app works on all apps. However, running Rosetta in MPI mode is recommended over using batch processing using Qsub. If you can get MPI to work on your cluster, use it instead. QsubClusterSetup is made to be applicable to all apps and all clusters. If you find it does not work for yours, please report it on the bugtracker.

Describe how to get the best use out of the protocol. Does it not require constraints, but work better with them? Do you need to remember -ex1 -ex2 to get much out of it?

Expected Outputs

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

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?

New things since last release

If you've made improvements, note them here.