PyRosetta workshops are NOW in Jupyter Notebook format AT https://rosettacommons.github.io/PyRosetta.notebooks/. The expanded set of Jupyter Notebook workshops can be used in a free Google Colaboratory environment or on a local machine. These workshops go step-by-step through the basics of PyRosetta, from an introduction to PyMOL, to accessing and manipulating protein structures in Rosetta, to development and design of simple AND ADVANCED protocols. Below is the old and DEPRECATED PyRosetta tutorials which is no longer supported. A variety of tutorials are provided here for your convenience. The main source of training for the use of PyRosetta is found in a set of workshops that go step-by-step through the basics of PyRosetta, from an introduction to PyMOL, to accessing and manipulating protein structures in Rosetta, to development and design of simple protocols. (Deprecated) PyRosetta WorkshopsSome of the PyRosetta Jupyter Notebooks are based on the deprecated PDF versions below, which are still available for download. The entire 3rd edition - PyRosetta4 Update of the workbook is also available for purchase through Amazon. For the most up-to-date set of workshops, please go to the PyRosetta Notebooks GitHub page or public repository. ![]() The PyRosetta Interactive Platform for Protein Structure Prediction and Design: A Set of Educational Module PrefaceThe Preface to the workshops with information about the team that designed PyRosetta. Workshop #1: PyMOLA brief introduction to PyMOL and its use as a tool for structural biology. PyMOL is the preferred visualization tool to accompany these Workshops and the sample scripts. See also the PyMOL_Mover Tutorial. Workshop #2: PyRosettaAn introduction to PyRosetta as a tool for structural biology. This tutorial covers Workshop #3: PyRosetta ScoringAn introduction to Rosetta scoring as a tool for modeling energetic characteristics of molecules. This tutorial covers Workshop #4: PyRosetta FoldingAn introduction to conformation space sampling with PyRosetta, specifically in the context of low-resolution (centroid) folding algorithms. This tutorial covers the centroid representation of molecules, general Monte Carlo algorithms, Workshop #5: PyRosetta RefinementAn introduction to Rosetta full-atom conformation space sampling. This tutorial covers many Workshop #6: Packing & DesignAn introduction to side-chain conformation sampling using rotamer libraries (termed packing) and PyRosetta's design capabilities. This tutorial covers the Workshop #7: DockingAn introduction to Rosetta docking using the PyRosetta supports the validated Rosetta docking protocol and is useful for applications beyond protein–protein docking that are not covered in the this workshop. Please consult the sample scripts Workshop #8: Loop ModelingAn introduction to protein loop modeling using the Cyclic Coordinate Descent (CCD) and algorithm. This tutorial covers loop modeling Workshop #9: Custom Movers & Energy MethodsAn introduction to utilizing Python's object-oriented features to create custum PyRosetta Appendix A: Command ReferenceA brief command reference for PyRosetta commands. Currently, an enumeration of all the working objects and methods would take too much time. Please use the built-in help and tab-completion features of an interactive Python environment, such as IPython, to explore PyRosetta on your own. Also consult our documentation for additional suggestions and our FAQ. Appendix B: Residue Parameter FilesA brief explanation of the Appendix C: Cleaning pdb FilesExamples of various methods of preparing Appendix D: Links to Online HelpA list of helpful Internet sites. A Coda concluding the PyRosetta Workbook. Coming to the Third Edition SoonWorkshop #10: Nucleic AcidsA tutorial planned for the 3rd edition of the Workshops. Workshop #11: Ligands & Non-canonical Amino AcidsA tutorial planned for the 3rd edition of the Workshops. Workshop #12: NMR ConstraintsA tutorial planned for the 3rd edition of the Workshops. Workshop #13: CarbohydratesA tutorial planned for the 3rd edition of the Workshops. Workshop #14: Membrane ProteinsA tutorial planned for the 3rd edition of the Workshops. Other Printable TutorialsRosettaCarbohydrate Tutorial/DemoThis document, written by Jason W. Labonte, uses IPython to demonstrate how to work with carbohydrates in PyRosetta. Web TutorialsPyMOL_MoverA new feature beginning with PyRosetta 2.0 is the PyMOL_Mover, an object built specifically to transmit data directly to PyMOL for quick visualizations. Workshops #2 and #3 introduce a few PyMOL_Mover features; for further options, please use the PyMOL_Mover Tutorial. Ligand Applications & PDB FilesThe sample script For DNA–protein applications, use the sample script Tutorial VideosSlide PresentationYou may also wish to view the slides to a presentation given at the 2012 RosettaCON, which covers some material not yet available in the workshops. PyRosetta Installation DocumentA document outlining the process required to get PyRosetta up and running on your machine. |
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