We have developed 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. 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.PyMOL_MoverA new feature for PyRosetta2.0 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.Workshop #2: PyRosettaAn introduction to PyRosetta as a tool for structural biology. This tutorial covers the Pose object, how to obtain and load PDB files, and how to probe PyRosetta for structural data. The sample scriptpose_structure.py accompanies this workshop.Workshop #3: PyRosetta ScoringAn introduction to Rosetta scoring as a tool for modeling energetic characteristics of molecules. This tutorial covers the ScoreFunction object and several of the most important score terms (ScoreType objects). The sample scriptpose_scoring.py accompanies this workshop.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, MonteCarlo objects, Movers, and the technique of fragment insertion. The sample scriptfolding.py accompanies this workshop.Workshop #5: PyRosetta RefinementAn introduction to Rosetta fullatom conformation space sampling. This tutorial covers many Mover classes including MinMover, SmallMover, ShearMover, RepeatMover, SequenceMover, and TrialMover. The sample scriptsmovemap.py and refinement.py accompany this workshop.Workshop #6: Packing & DesignAn introduction to side-chain conformation sampling using rotamer libraries (termed packing) and PyRosetta's design capabilities. This tutorial covers the PackerTask, PackRotamersMover, and resfile syntax. The sample scriptpacker_task.py accompanies this workshop. The tool script generate_resfile.py eases usage of PackerTask objects.Workshop #7: DockingAn introduction to Rosetta docking using the DockingProtocol. This tutorial covers the FoldTree object, protein-protein docking, and the PyJobDistributor. The sample scriptsfold_tree.py and docking.py accompany this workshop.Additional DockingPyRosetta supports the validated Rosetta DockingProtocol and is useful for applications beyond protein-protein docking that are not covered in these workshops. Please consult the sample scriptsdna_interface.py, ligand_interface.py, and ala_scan.py for more information.Workshop #8: Loop ModelingAn introduction to protein loop modeling using the Cyclic Coordinate Descent algorithm. This tutorial covers loop modeling FoldTrees and CCD loop closure. the sample scriptsfold_tree.py and loop_modeling.py accompany this workshop.Ligand Applications and PDB filesThe sample script ligand_interface.py outlines several of the objects available in PyRosetta for modeling protein-ligand interactions. Obtaining and reading ligands in PyRosetta can be difficult so we provided a tutorial to guide users through the process.For DNA-protein applications, use the sample script dna_interface.py as a starting point (you will not need to alter the chemical database as is necessary for using ligands). Appendix A: Command ReferenceA brief command reference for PyRosetta commands. Currently, an enumeration of the working objects and methods would take too much time. Please use the built-in help and tab-completion to explore PyRosetta on your own. Consult our documentation for additional suggestions and help.\Appendix B: Residue Parameter FilesA brief explanation of the .params file syntax used to store chemical information in PyRosetta. If you are using ligands in PyRosetta, please consult the sample scriptligand_interface.py and the tool scripts mutants.py, molfile2params, and load_ligand.py.Appendix C: Cleaning pdb FilesExamples of various methods of preparing pdb files for use in PyRosetta.Appendix D: Links to Online Help  The PyRosetta Tutorial can also be downloaded free as individual chapters from the links below.
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