viromic / pyrosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

PyRosetta Workshops

Getting Started

Students

Step 1: Sign in to Google Drive.

Step 2: Make a new folder called “PyRosetta” in your top level directory on Google Drive.

Step 3: Get your PyRosetta license.

Step 4: Download the Linux PyRosetta package that is called "Python-3.6.MinSizeRel".

Step 5: Upload the Linux PyRosetta package (.tar file) to the PyRosetta folder in your Google Drive.

Step 6: Go to https://github.com/RosettaCommons/PyRosetta.notebooks and download the ZIP folder.

Step 7: Upload either (or both) the student-notebooks folder and the notebooks folder to the top-level directory of your Google Drive.

Step 8: From the notebooks or student-notebooks folder, open up “01.01-PyRosetta-Google-Drive-Setup.ipynb” in Google Colab by right-clicking, going under “Open With…” and clicking Google Colaboratory.

Step 9: Follow steps to install PyRosetta. You will see a bar and a lot of output, and it should take 10-15 minutes. Note: You only need to do this once since this installation will be associated with your Google Drive account.

Step 10: Open up “01.02-PyRosetta-Google-Drive-Usage-Example.ipynb” in Colab to make sure that PyRosetta was installed properly. You are now ready to move on to the other notebooks!

Instructors

Step 1: Please install extensions nbgrader and nbpages.

Step 2: Make any changes to the workshops in the "notebooks" folder. (You can follow the directions for students and edit them in Google Colab or on your own computer using a Jupyter Notebooks browser.)

Step 3: When you are done making changes, run make-student-nb.bash to automatically generate the student notebooks in a separate folder, the table of contents you see below, and the keyword index. The student notebooks are copies of the instructor's version that have omitted solutions.

Table of Contents

Keyword Index

Chapter 1.0 How to Get Started

• 1.1 PyRosetta Google Drive Setup
• 1.2 PyRosetta Google Drive Usage Example
• 1.3 How to Get PyRosetta on Your Personal Computer

Chapter 2.0 Introduction to PyRosetta

• 2.1 Pose Basics
• 2.2 Working with Pose residues
• 2.3 Accessing PyRosetta Documentation
• 2.4 Getting spatial features from a Pose
• 2.5 Protein Geometry
• 2.6 Visualization with the PyMOLMover
• 2.7 RosettaScripts in PyRosetta
• 2.8 Visualization and pyrosetta.distributed.viewer

Chapter 3.0 Rosetta Energy Score Functions

• 3.1 Score Function Basics
• 3.2 Practice: Analyzing energy between residues
• 3.3 Energies and the PyMOL Mover

Chapter 4.0 Introduction to Folding

• 4.1 Basic Folding Algorithm
• 4.2 Low-Res Scoring and Fragments

Chapter 5.0 Structure Refinement

• 5.1 High-Resolution Movers
• 5.2 Refinement Protocol

Chapter 6.0 Packing & Design

• 6.1 Side Chain Conformations and Dunbrack Energies
• 6.2 Packing and Relax
• 6.3 Protein Design with a Resfile and FastRelax
• 6.4 Protein Design 2
• 6.5 HBNet Before Design
• 6.6 De Novo Parametric Backbone Design
• 6.7 De Novo Protein Design with PyRosetta

Chapter 7.0 Docking

• 7.1 Fast Fourier Transform Based Docking via ZDOCK
• 7.2 Docking Moves in Rosetta
• 7.3 Ligand Refinement in PyRosetta (a.k.a. High-Resolution Local Docking) Using the ligand.wts Scorefunction
• 7.4 Global Ligand Docking using XMLObjects Using the ref2015.wts Scorefunction
• 7.5 GALigandDock Protocol with pyrosetta.distributed Using the beta_cart.wts Scorefunction

Chapter 9.0 Working With Symmetry

Chapter 10.0 Working With Density

Chapter 11.0 Working With Antibodies

• 11.1 RosettaAntibody Framework
• 11.2 RosettaAntibodyDesign

Chapter 12.0 RosettaCarbohydrates

• 12.1 RosettaCarbohydrates: Trees, Selectors and Movers
• 12.2 RosettaCarbohydrates: Modeling and Design

Chapter 13.0 RNA in PyRosetta

Chapter 15.0 Running Rosetta in Parellel

• 15.1 Distributed analysis example: exhaustive ddG PSSM
• 15.2 Distributed computation example: miniprotein design
• 15.3 Example of Using PyRosetta with GNU Parallel
• 15.4 Examples Using the dask Module
• 15.5 Part I: Parallelized Global Ligand Docking with pyrosetta.distributed