{
"cells": [
{
"cell_type": "markdown",
"id": "187c637c",
"metadata": {},
"source": [
"# [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks)\n",
"\n",
"\n",
"## [Chapter 1.0 How to Get Started](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.00-How-to-Get-Started.ipynb)\n",
"- [Students](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.00-How-to-Get-Started.ipynb#Students)\n",
"- [Instructors](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.00-How-to-Get-Started.ipynb#Instructors)\n",
"\n",
"### [1.1 How to Get PyRosetta on Your Personal Computer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.01-How-to-Get-Local-PyRosetta.ipynb)\n",
"- [Download the main necessary packages to work locally on your machine](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.01-How-to-Get-Local-PyRosetta.ipynb#Download-the-main-necessary-packages-to-work-locally-on-your-machine)\n",
" - [Python 3.9 (and preferably IPython for tab-completion)](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.01-How-to-Get-Local-PyRosetta.ipynb#Python-3.9-(and-preferably-IPython-for-tab-completion))\n",
" - [PyMOL](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.01-How-to-Get-Local-PyRosetta.ipynb#PyMOL)\n",
" - [PyRosetta-3.9.Release](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.01-How-to-Get-Local-PyRosetta.ipynb#PyRosetta-3.9.Release)\n",
"\n",
"### [1.2 Jupyter Notebooks, Python, and Google Colaboratory](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.02-Notebooks-Python-Colab.ipynb)\n",
"* Links\n",
" - [tutorial](https://nbviewer.jupyter.org/github/jckantor/CBE20255/blob/master/notebooks/00.01-Getting-Started-with-Jupyter-Notebooks-and-Python.ipynb)\n",
"\n",
"### [1.3 Frequently Asked Questions/Troubleshooting Tips](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.03-FAQ.ipynb)\n",
"\n",
"\n",
"## [Chapter 2.0 Introduction to PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.00-Introduction-to-PyRosetta.ipynb)\n",
"* Links\n",
" - [PyRosetta book](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8)\n",
"\n",
"### [2.1 Pose Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.01-Pose-Basics.ipynb)\n",
"- [Loading in a PDB File ##](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.01-Pose-Basics.ipynb#Loading-in-a-PDB-File-##)\n",
"- [What is a Pose?](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.01-Pose-Basics.ipynb#What-is-a-Pose?)\n",
" - [Exercise 1: Inspecting pose sequences](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.01-Pose-Basics.ipynb#Exercise-1:-Inspecting-pose-sequences)\n",
" - [Bonus Exercise 1: Identifying differences in sequences](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.01-Pose-Basics.ipynb#Bonus-Exercise-1:-Identifying-differences-in-sequences)\n",
"\n",
"### [2.2 Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.02-Working-with-Pose-Residues.ipynb)\n",
"- [Exercise 2: Residue objects](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.02-Working-with-Pose-Residues.ipynb#Exercise-2:-Residue-objects)\n",
"\n",
"### [2.3 Accessing PyRosetta Documentation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb)\n",
"- [Exercise 3: Python Object Help](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb#Exercise-3:-Python-Object-Help)\n",
"- [Exercise 4: Some residue commands](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb#Exercise-4:-Some-residue-commands)\n",
"\n",
"### [2.4 Getting spatial features from a Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb)\n",
"- [References](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb#References)\n",
"\n",
"### [2.5 Protein Geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.05-Protein-Geometry.ipynb)\n",
"- [Rosetta Database Files](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.05-Protein-Geometry.ipynb#Rosetta-Database-Files)\n",
" - [Exercise 5: Calculating psi angle](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.05-Protein-Geometry.ipynb#Exercise-5:-Calculating-psi-angle)\n",
"- [Manipulating Protein Geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.05-Protein-Geometry.ipynb#Manipulating-Protein-Geometry)\n",
"\n",
"### [2.6 Visualization with the `PyMOLMover`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb)\n",
"- [Exercise 7: Visualizing changes in backbone angles](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#Exercise-7:-Visualizing-changes-in-backbone-angles)\n",
"- [Additional Exercises ##](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#Additional-Exercises-##)\n",
" - [Analyzing Amino Acid Patterns](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#Analyzing-Amino-Acid-Patterns)\n",
" - [Active Site Residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#Active-Site-Residues)\n",
"- [Answers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#Answers)\n",
" - [Exercise 6](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#Exercise-6)\n",
"- [References](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb#References)\n",
"* Links\n",
" - [Ramachandran plot](http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.1b.html)\n",
" - [Richardson's Anatomy and Taxonomy of Protein Structure](http://kinemage.biochem.duke.edu/teaching/anatax/)\n",
"\n",
"### [2.7 Visualization with the `PyMOLMover`, PyRosetta ColabPyMOL integration](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.07-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration.ipynb)\n",
"\n",
"### [2.8 RosettaScripts in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb)\n",
"- [Running Whole Protocols via RosettaScriptsParser](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb#Running-Whole-Protocols-via-RosettaScriptsParser)\n",
"- [Running via XMLObjects and strings](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb#Running-via-XMLObjects-and-strings)\n",
"- [Constructing Rosetta objects using XMLObjects](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb#Constructing-Rosetta-objects-using-XMLObjects)\n",
" - [Constructing from single section](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-RosettaScripts-in-PyRosetta.ipynb#Constructing-from-single-section)\n",
"\n",
"### [2.9 Visualization and `pyrosetta.distributed.viewer`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.09-Visualization-and-pyrosetta.distributed.viewer.ipynb)\n",
" - [Available `viewer` objects:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.09-Visualization-and-pyrosetta.distributed.viewer.ipynb#Available-`viewer`-objects:)\n",
" - [Available `viewer.presets` objects:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.09-Visualization-and-pyrosetta.distributed.viewer.ipynb#Available-`viewer.presets`-objects:)\n",
" - [`viewer` objects contain docstrings as user documentation:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.09-Visualization-and-pyrosetta.distributed.viewer.ipynb#`viewer`-objects-contain-docstrings-as-user-documentation:)\n",
" - [`viewer.presets` objects contain docstrings as brief descriptions of each preset visualization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.09-Visualization-and-pyrosetta.distributed.viewer.ipynb#`viewer.presets`-objects-contain-docstrings-as-brief-descriptions-of-each-preset-visualization)\n",
"\n",
"\n",
"## [Chapter 3.0 Rosetta Energy Score Functions](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.00-Rosetta-Energy-Score-Functions.ipynb)\n",
"* Links\n",
" - [PyRosetta Workshops](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8)\n",
"\n",
"### [3.1 Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb)\n",
"- [Practice: List the terms in the energy function and their relative weights](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb#Practice:-List-the-terms-in-the-energy-function-and-their-relative-weights)\n",
"- [Custom energy functions](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb#Custom-energy-functions)\n",
"- [Energy Breakdown](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb#Energy-Breakdown)\n",
"* Links\n",
" - [documentation](https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.toolbox.atom_pair_energy.html?highlight=etable_atom_pair_energies#pyrosetta.toolbox.atom_pair_energy.etable_atom_pair_energies)\n",
"\n",
"### [3.2 Practice: Analyzing energy between residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.02-Analyzing-energy-between-residues.ipynb)\n",
"\n",
"### [3.3 Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb)\n",
"- [References](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb#References)\n",
"\n",
"\n",
"## [Chapter 4.0 Introduction to Folding](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.00-Introduction-to-Folding.ipynb)\n",
"* Links\n",
" - [PyRosetta book](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8)\n",
"\n",
"### [4.1 Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb)\n",
"- [Building the Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb#Building-the-Pose)\n",
"- [Building A Basic *de Novo* Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb#Building-A-Basic-*de-Novo*-Folding-Algorithm)\n",
" - [Step 1: Random Move](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb#Step-1:-Random-Move)\n",
" - [Step 2: Scoring Move](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb#Step-2:-Scoring-Move)\n",
" - [Step 3: Accepting/Rejecting Move](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb#Step-3:-Accepting/Rejecting-Move)\n",
" - [Step 4: Execution](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb#Step-4:-Execution)\n",
" - [Exercise 1: Comparing to Alpha Helices](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb#Exercise-1:-Comparing-to-Alpha-Helices)\n",
" - [Exercise 2: Optimizing Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb#Exercise-2:-Optimizing-Algorithm)\n",
"\n",
"### [4.2 Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb)\n",
"- [Low-Resolution (Centroid) Scoring](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Low-Resolution-(Centroid)-Scoring)\n",
" - [SwitchResidueTypeSetMover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#SwitchResidueTypeSetMover)\n",
" - [Exercise 1: Centroid Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Exercise-1:-Centroid-Folding-Algorithm)\n",
" - [Note about `Movers`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Note-about-`Movers`)\n",
"- [Protein Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Protein-Fragments)\n",
" - [Using FragmentMover and MoveMap](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Using-FragmentMover-and-MoveMap)\n",
" - [Exercise 2: Fragment Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Exercise-2:-Fragment-Folding-Algorithm)\n",
" - [Programming Exercises](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb#Programming-Exercises)\n",
"\n",
"\n",
"## [Chapter 5.0 Structure Refinement](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.00-Structure-Refinement.ipynb)\n",
"* Links\n",
" - [PyRosetta book](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8)\n",
"\n",
"### [5.1 High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb)\n",
"- [Small and Shear Moves](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb#Small-and-Shear-Moves)\n",
" - [Test your mover by applying it to your pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb#Test-your-mover-by-applying-it-to-your-pose)\n",
" - [Comparing small and shear movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb#Comparing-small-and-shear-movers)\n",
"- [Minimization Moves](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb#Minimization-Moves)\n",
"- [Monte Carlo Object](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb#Monte-Carlo-Object)\n",
"- [Trial Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb#Trial-Mover)\n",
"- [Sequence and Repeat Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb#Sequence-and-Repeat-Movers)\n",
"\n",
"### [5.2 Refinement Protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.02-Refinement-Protocol.ipynb)\n",
"- [Programming Exercises](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.02-Refinement-Protocol.ipynb#Programming-Exercises)\n",
"- [Thought Questions](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.02-Refinement-Protocol.ipynb#Thought-Questions)\n",
"\n",
"\n",
"## [Chapter 6.0 Packing & Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.00-Introduction-to-Packing-and-Design.ipynb)\n",
"* Links\n",
" - [PyRosetta book](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8)\n",
"\n",
"### [6.1 Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb)\n",
"\n",
"### [6.2 Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb)\n",
"- [Imports](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Imports)\n",
"- [Intitlialization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Intitlialization)\n",
"- [Import and copy pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Import-and-copy-pose)\n",
"- [Setup a Normal TaskFactory](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Setup-a-Normal-TaskFactory)\n",
"- [Setup The Packer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Setup-The-Packer)\n",
"- [Regional Packing](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Regional-Packing)\n",
" - [Restrict to our selection](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Restrict-to-our-selection)\n",
" - [Reset the pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Reset-the-pose)\n",
"- [Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Design)\n",
" - [Set and Run](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Set-and-Run)\n",
"- [Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Relax)\n",
" - [Regional Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Regional-Relax)\n",
" - [Regional Relax - Classic](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb#Regional-Relax---Classic)\n",
"\n",
"### [6.3 Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb)\n",
"- [Overview](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Overview)\n",
" - [Initialize PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Initialize-PyRosetta)\n",
"- [Design strategy:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Design-strategy:)\n",
" - [Analysis](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb#Analysis)\n",
"\n",
"### [6.4 Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.04-Protein-Design-2.ipynb)\n",
"- [Initialize PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.04-Protein-Design-2.ipynb#Initialize-PyRosetta)\n",
"- [Design strategy](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.04-Protein-Design-2.ipynb#Design-strategy)\n",
"- [*Design Challenge*:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.04-Protein-Design-2.ipynb#*Design-Challenge*:)\n",
"\n",
"### [6.5 HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb)\n",
"- [Setting Designable Residues:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb#Setting-Designable-Residues:)\n",
"- [Running HBNet](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb#Running-HBNet)\n",
"- [Finishing Design:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb#Finishing-Design:)\n",
"- [We made it...?](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb#We-made-it...?)\n",
"- [But wait, there's more??](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb#But-wait,-there's-more??)\n",
"- [Advice for using this in the wild](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb#Advice-for-using-this-in-the-wild)\n",
"- [Thought Question](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb#Thought-Question)\n",
"\n",
"### [6.6 *De Novo* Parametric Backbone Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb)\n",
"- [Overview](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#Overview)\n",
"- [Changing omega0](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#Changing-omega0)\n",
"- [MakeBundle Mover in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#MakeBundle-Mover-in-PyRosetta)\n",
"- [Conclusion](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#Conclusion)\n",
"- [References:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb#References:)\n",
"\n",
"### [6.7 *De Novo* Protein Design with PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.07-Introduction-to-DeNovo-protein-design.ipynb)\n",
"- [Design Strategy](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.07-Introduction-to-DeNovo-protein-design.ipynb#Design-Strategy)\n",
"- [*De Novo* Protein Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.07-Introduction-to-DeNovo-protein-design.ipynb#*De-Novo*-Protein-Design)\n",
"- [Analysis:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.07-Introduction-to-DeNovo-protein-design.ipynb#Analysis:)\n",
"\n",
"### [6.8 **Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb)\n",
"- [**Section Contributors:**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#**Section-Contributors:**)\n",
" - [Set up notebook](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#Set-up-notebook)\n",
" - [Loading structures](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#Loading-structures)\n",
"- [**Step 1. Prepare the starting structure with FastRelax()**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#**Step-1.-Prepare-the-starting-structure-with-FastRelax()**)\n",
" - [Writing Function in Python](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#Writing-Function-in-Python)\n",
"- [**Step 2. Write the function for mutation**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#**Step-2.-Write-the-function-for-mutation**)\n",
" - [**Step 3. unbind()**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#**Step-3.-unbind()**)\n",
"- [**Step 4. wildtype()**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#**Step-4.-wildtype()**)\n",
"- [**Step 5. Integrate functions for mutate and output**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#**Step-5.-Integrate-functions-for-mutate-and-output**)\n",
"- [**Step 6. Loop through interface positions**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#**Step-6.-Loop-through-interface-positions**)\n",
"- [**Analysis of binding data**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb#**Analysis-of-binding-data**)\n",
"* Links\n",
" - [ pareto-optimal method by Nivon, Morreti, and Baker ](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059004)\n",
"\n",
"\n",
"## [Chapter 7.0 Docking](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.00-Protein-Docking.ipynb)\n",
"* Links\n",
" - [PyRosetta book](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8)\n",
"\n",
"### [7.1 Fast Fourier Transform Based Docking via ZDOCK](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.ipynb)\n",
"\n",
"### [7.2 Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb)\n",
"- [Rigid-body transformations and Fold Trees](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Rigid-body-transformations-and-Fold-Trees)\n",
"- [RigidBody Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#RigidBody-Movers)\n",
"- [Low-Resolution Docking via RosettaDock](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Low-Resolution-Docking-via-RosettaDock)\n",
"- [Job Distributor](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Job-Distributor)\n",
"- [High-Resolution Docking](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#High-Resolution-Docking)\n",
"- [Docking Funnel](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Docking-Funnel)\n",
"- [Programming Exercises](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb#Programming-Exercises)\n",
"\n",
"\n",
"## [Chapter 8.0 Ligand Refinement in PyRosetta (a.k.a. High-Resolution Local Docking) Using the `ligand.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.00-Ligand-Docking-PyRosetta.ipynb)\n",
"\n",
"### [8.1 Global Ligand Docking using `XMLObjects` Using the `ref2015.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.01-Ligand-Docking-XMLObjects.ipynb)\n",
"\n",
"### [8.2 `GALigandDock` Protocol with `pyrosetta.distributed` Using the `beta_cart.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb)\n",
" - [Inspect the scores for the `GALigandDock` trajectories:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb#Inspect-the-scores-for-the-`GALigandDock`-trajectories:)\n",
" - [Now that we have performed `GALigandDock`, we can plot the ligand binding energy landscape:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb#Now-that-we-have-performed-`GALigandDock`,-we-can-plot-the-ligand-binding-energy-landscape:)\n",
"\n",
"\n",
"## [Chapter 9.0 Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb)\n",
"- [Lever-Arm Effect](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Lever-Arm-Effect)\n",
"- [Fold Tree](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Fold-Tree)\n",
" - [Fold Tree (from scratch)](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Fold-Tree-(from-scratch))\n",
" - [Fold Tree (using functions)](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Fold-Tree-(using-functions))\n",
" - [Single loop](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Single-loop)\n",
" - [Multiple Loops](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Multiple-Loops)\n",
" - [Exercises](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Exercises)\n",
"- [Cyclic Coordination Descent (CCD) Loop Closure](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Cyclic-Coordination-Descent-(CCD)-Loop-Closure)\n",
"- [Loop Building](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Loop-Building)\n",
"- [High-Resolution Loop Protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#High-Resolution-Loop-Protocol)\n",
"- [Kinematic Closure (KIC) Protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Kinematic-Closure-(KIC)-Protocol)\n",
"- [Simultaneous Loop Modeling and Docking](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb#Simultaneous-Loop-Modeling-and-Docking)\n",
"* Links\n",
" - [Rosetta Commons docs page](https://www.rosettacommons.org/docs/latest/Home)\n",
"\n",
"### [9.1 Using Rosetta Gen KIC](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb)\n",
"- [Step 1: Preparing to close loop](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Step-1:-Preparing-to-close-loop)\n",
" - [Slice Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Slice-Pose)\n",
" - [Connect two objects with arbitrary residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Connect-two-objects-with-arbitrary-residues)\n",
"- [Step 2: Initial GeneralizedKIC setup](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Step-2:-Initial-GeneralizedKIC-setup)\n",
"- [Step 3 Set GenKic parameters](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Step-3-Set-GenKic-parameters)\n",
"- [Step 3: Setting GeneralizedKIC perturbers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Step-3:-Setting-GeneralizedKIC-perturbers)\n",
"- [Step 4: Apply to pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Step-4:-Apply-to-pose)\n",
"- [Step 5: Filtering solutions to discard bad geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Step-5:-Filtering-solutions-to-discard-bad-geometry)\n",
" - [Loop bump check](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Loop-bump-check)\n",
" - [Set rama prepro](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Set-rama-prepro)\n",
"- [Step 6 Apply Perturbers and Filters and run GK](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb#Step-6-Apply-Perturbers-and-Filters-and-run-GK)\n",
"* Links\n",
" - [Accurate de novo design of hyperstable constrained peptides](https://www.ncbi.nlm.nih.gov/pubmed/27626386)\n",
" - [Comprehensive computational design of ordered peptide macrocycles](https://www.ncbi.nlm.nih.gov/pubmed/29242347)\n",
"\n",
"\n",
"## [Chapter 10.0 Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb)\n",
"- [Creating a SymDef file](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb#Creating-a-SymDef-file)\n",
"- [Setup a Symmetrized Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb#Setup-a-Symmetrized-Pose)\n",
"- [Running Protocols with Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb#Running-Protocols-with-Symmetry)\n",
"- [Conclusions](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb#Conclusions)\n",
"\n",
"\n",
"## [Chapter 11.0 Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb)\n",
"- [Creating a Density Map](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb#Creating-a-Density-Map)\n",
"- [Setup for Density Scoring](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb#Setup-for-Density-Scoring)\n",
"- [Conclusion](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb#Conclusion)\n",
"\n",
"\n",
"## [Chapter 12.0 Working With Antibodies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.00-Working-With-Antibodies.ipynb)\n",
"- [Overview](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.00-Working-With-Antibodies.ipynb#Overview)\n",
"- [IgG](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.00-Working-With-Antibodies.ipynb#IgG)\n",
"- [CDRs](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.00-Working-With-Antibodies.ipynb#CDRs)\n",
"- [Antibody Numbering Schemes](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.00-Working-With-Antibodies.ipynb#Antibody-Numbering-Schemes)\n",
"\n",
"### [12.1 RosettaAntibody Framework](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb)\n",
"- [Imports](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Imports)\n",
"- [Intitlialization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Intitlialization)\n",
"- [Import and copy pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Import-and-copy-pose)\n",
"- [AntibodyInfo](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#AntibodyInfo)\n",
"- [Basic AntibodyInfo Access](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Basic-AntibodyInfo-Access)\n",
" - [AntibodyEnumManager](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#AntibodyEnumManager)\n",
" - [CDR Clusters](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#CDR-Clusters)\n",
" - [Numbering Scheme Translation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Numbering-Scheme-Translation)\n",
" - [Sequence](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Sequence)\n",
" - [Other AntibodyInfo functions](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Other-AntibodyInfo-functions)\n",
" - [AntibodyInfo Deprecated Functions](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#AntibodyInfo-Deprecated-Functions)\n",
"- [Antibody Util and SimpleMetrics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Antibody-Util-and-SimpleMetrics)\n",
" - [Function: select_epitope_residues()](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Function:-select_epitope_residues())\n",
" - [SasaMetric, TotalEnergyMetric, SelectedResiduesPyMOLMetric](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#SasaMetric,-TotalEnergyMetric,-SelectedResiduesPyMOLMetric)\n",
" - [PerResidueSasaMetric](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#PerResidueSasaMetric)\n",
"- [Other Useful Antibody Tools](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Other-Useful-Antibody-Tools)\n",
" - [AntibodyRegionSelector](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#AntibodyRegionSelector)\n",
" - [Other](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#Other)\n",
"- [References](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb#References)\n",
"* Links\n",
" - [Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb)\n",
" - [Contents](toc.ipynb)\n",
" - [Index](index.ipynb)\n",
" - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb)\n",
"\n",
"### [12.2 RosettaAntibodyDesign](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb)\n",
"- [Imports](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Imports)\n",
"- [Intitlialization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Intitlialization)\n",
" - [Tut A1. Sequence Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-A1.-Sequence-Design)\n",
" - [Tut A2. Graft Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-A2.-Graft-Design)\n",
" - [Tut A3. Basic De-novo run](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-A3.-Basic-De-novo-run)\n",
" - [Tut A4. RAbD Framework Components](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-A4.-RAbD-Framework-Components)\n",
" - [Challenge: Custom Design Protocol in code](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Challenge:-Custom-Design-Protocol-in-code)\n",
"- [Tutorial B: Optimizing Interface Energy (opt-dG)](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tutorial-B:-Optimizing-Interface-Energy-(opt-dG))\n",
" - [Tut B2. Optimizing Interface Energy and Total Score (opt-dG and opt-E)](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-B2.-Optimizing-Interface-Energy-and-Total-Score-(opt-dG-and-opt-E))\n",
"- [Tutorial C: Towards DeNovo Design: Integrated Dock/Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tutorial-C:-Towards-DeNovo-Design:-Integrated-Dock/Design)\n",
" - [Tut C2. Auto Epitope Constraints](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-C2.-Auto-Epitope-Constraints)\n",
" - [Tut C3. Specific Residue Epitope Constraints](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-C3.-Specific-Residue-Epitope-Constraints)\n",
"- [Tutorial D: Advanced Settings and CDR Instruction File Customization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tutorial-D:-Advanced-Settings-and-CDR-Instruction-File-Customization)\n",
" - [Tut D2. Dissallow AAs and the Resfile](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-D2.-Dissallow-AAs-and-the-Resfile)\n",
" - [Tut D3. Mintype](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-D3.-Mintype)\n",
" - [Tut D4. Framework Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-D4.-Framework-Design)\n",
" - [Tut D5. H3 Stem, kT, and Sequence variablility.](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb#Tut-D5.-H3-Stem,-kT,-and-Sequence-variablility.)\n",
"* Links\n",
" - [Rosetta Antibody Design (RAbD): A General Framework for Computational Antibody Design, PLOS Computational Biology, 4/27/2018](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006112)\n",
" - [recent clustering](https://www.ncbi.nlm.nih.gov/pubmed/21035459)\n",
" - [PyIgClassify Server](http://dunbrack2.fccc.edu/pyigclassify/)\n",
" - [Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb)\n",
" - [Contents](toc.ipynb)\n",
" - [Index](index.ipynb)\n",
" - [Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb)\n",
"\n",
"\n",
"## [Chapter 13.0 RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb)\n",
"- [Carbohydrate Chemistry Background](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Carbohydrate-Chemistry-Background)\n",
"- [Initialization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Initialization)\n",
"- [Creating Saccharides from Sequence](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Creating-Saccharides-from-Sequence)\n",
" - [Anomers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Anomers)\n",
" - [Linear Oligosaccharides & IUPAC Sequences](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Linear-Oligosaccharides-&-IUPAC-Sequences)\n",
" - [General Residue Information](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#General-Residue-Information)\n",
"- [Exploring Carbohydrate Structure](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Exploring-Carbohydrate-Structure)\n",
" - [Creating Saccharides from a PDB file](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Creating-Saccharides-from-a-PDB-file)\n",
" - [RingConformers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#RingConformers)\n",
"- [Modified Sugars, Branched Oligosaccharides, & `.pdb` File `LINK` Records](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Modified-Sugars,-Branched-Oligosaccharides,-&-`.pdb`-File-`LINK`-Records)\n",
"- [N- and O-Linked Glycans](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#N--and-O-Linked-Glycans)\n",
" - [Glycosylation by function](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Glycosylation-by-function)\n",
"- [Conclusion](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb#Conclusion)\n",
"\n",
"### [13.1 RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb)\n",
"- [Imports](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Imports)\n",
"- [Intitlialization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Intitlialization)\n",
"- [Object Exploration: GlycanTreeSet, CarbohydrateInfo, and the GlycanInfoMover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Object-Exploration:-GlycanTreeSet,-CarbohydrateInfo,-and-the-GlycanInfoMover)\n",
" - [GlycanTree and GlycanNode](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#GlycanTree-and-GlycanNode)\n",
" - [CarbohydrateInfo](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#CarbohydrateInfo)\n",
"- [GlycanInfoMover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#GlycanInfoMover)\n",
" - [Branched Connections](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Branched-Connections)\n",
" - [MoveMapFactory vs MoveMap creation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#MoveMapFactory-vs-MoveMap-creation)\n",
"- [Glycan Residue Selectors](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Glycan-Residue-Selectors)\n",
" - [All Carbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#All-Carbohydrates)\n",
" - [Branch Selection](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Branch-Selection)\n",
" - [GlycanLayerSelector](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#GlycanLayerSelector)\n",
" - [GlycanSequonSelector](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#GlycanSequonSelector)\n",
" - [RandomGlycanFoliageSelector](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RandomGlycanFoliageSelector)\n",
"- [Glycan Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Glycan-Movers)\n",
" - [Correcting Structures](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Correcting-Structures)\n",
" - [IdealizeAnomericHydrogens](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#IdealizeAnomericHydrogens)\n",
" - [RingPlaneFlipMover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#RingPlaneFlipMover)\n",
" - [Glycosylation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Glycosylation)\n",
" - [BB Sampling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#BB-Sampling)\n",
" - [BBSampler: SugarBBSampler](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#BBSampler:-SugarBBSampler)\n",
"- [Conclusion](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb#Conclusion)\n",
"* Links\n",
" - [Working With Glycans](https://www.rosettacommons.org/docs/latest/application_documentation/carbohydrates/WorkingWithGlycans)\n",
"\n",
"### [13.2 RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb)\n",
" - [A1.2 Design using the `N[^P][T]` motif](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb#A1.2-Design-using-the-`N[^P][T]`-motif)\n",
" - [A2. Adding a man5 glycan:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb#A2.-Adding-a-man5-glycan:)\n",
" - [A3. Modeling glycans](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb#A3.-Modeling-glycans)\n",
"- [Tutorial B: Using Glycan Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb#Tutorial-B:-Using-Glycan-Density)\n",
" - [B1. Calculating Density Fit](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb#B1.-Calculating-Density-Fit)\n",
" - [B2. Refinement into density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb#B2.-Refinement-into-density)\n",
" - [B3. Denovo building into Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb#B3.-Denovo-building-into-Density)\n",
"* Links\n",
" - [Working With Glycans](https://www.rosettacommons.org/docs/latest/application_documentation/carbohydrates/WorkingWithGlycans)\n",
"\n",
"\n",
"## [Chapter 14.0 RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb)\n",
"- [References](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#References)\n",
"- [Introduction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Introduction)\n",
"- [Exploring geometry for RNA ##](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Exploring-geometry-for-RNA-##)\n",
"- [Scoring RNA poses ##](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Scoring-RNA-poses-##)\n",
"- [Manipulating RNA poses ##](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Manipulating-RNA-poses-##)\n",
"- [Elements of RNA Structure Prediction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Elements-of-RNA-Structure-Prediction)\n",
" - [Generating an ideal A-form Helix](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Generating-an-ideal-A-form-Helix)\n",
" - [RNA Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#RNA-Fragments)\n",
" - [Minimizing Structures with RNA](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Minimizing-Structures-with-RNA)\n",
"- [Additional Exercises](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Additional-Exercises)\n",
" - [Post-mortem](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#Post-mortem)\n",
" - [FAR + FAR = FARFAR](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#FAR-+-FAR-=-FARFAR)\n",
"- [RNA Structure Prediction Protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb#RNA-Structure-Prediction-Protocol)\n",
"* Links\n",
" - [Fragment Assembly of RNA with Full Atom Refinement](https://www.rosettacommons.org/docs/latest/application_documentation/rna/rna-denovo)\n",
"\n",
"\n",
"## [Chapter 15.0 Modeling Membrane Proteins](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.00-Modeling-Membrane-Proteins.ipynb)\n",
"- [Background](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.00-Modeling-Membrane-Proteins.ipynb#Background)\n",
"- [Learning Objectives](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.00-Modeling-Membrane-Proteins.ipynb#Learning-Objectives)\n",
"- [Suggested Readings](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.00-Modeling-Membrane-Proteins.ipynb#Suggested-Readings)\n",
"- [Chapter Contributors](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.00-Modeling-Membrane-Proteins.ipynb#Chapter-Contributors)\n",
"\n",
"### [15.1 Setting up a membrane protein in the bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb)\n",
"- [Getting Started: Setting up the protein in the lipid bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Getting-Started:-Setting-up-the-protein-in-the-lipid-bilayer)\n",
" - [Option 1: Download a pre-transformed PDB from the OPM database](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Option-1:-Download-a-pre-transformed-PDB-from-the-OPM-database)\n",
" - [Option 2: Estimate the transmembrane spans and use this information to choose an orientation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Option-2:-Estimate-the-transmembrane-spans-and-use-this-information-to-choose-an-orientation)\n",
"- [Key Concepts for the membrane representation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Key-Concepts-for-the-membrane-representation)\n",
"- [Fold Tree](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb#Fold-Tree)\n",
"\n",
"### [15.2 Predicting the ∆∆G of single point mutations](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb)\n",
"- [Objectives](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb#Objectives)\n",
"- [PyRosetta Initialization & Setup](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb#PyRosetta-Initialization-&-Setup)\n",
"- [∆∆G of mutation calculations](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb#∆∆G-of-mutation-calculations)\n",
" - [TODO List](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb#TODO-List)\n",
"\n",
"\n",
"## [Chapter 16.0 Running Rosetta in Parallel](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.00-Running-PyRosetta-in-Parallel.ipynb)\n",
"* Links\n",
" - [Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation](https://doi.org/10.1002/pro.3721)\n",
"\n",
"### [16.1 Distributed analysis example: exhaustive ddG PSSM](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.01-PyData-ddG-pssm.ipynb)\n",
"- [Create test pose, initialize rosetta and pack](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.01-PyData-ddG-pssm.ipynb#Create-test-pose,-initialize-rosetta-and-pack)\n",
"- [Perform exhaustive point mutation and pack](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.01-PyData-ddG-pssm.ipynb#Perform-exhaustive-point-mutation-and-pack)\n",
"- [Job distribution via `multiprocessing`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.01-PyData-ddG-pssm.ipynb#Job-distribution-via-`multiprocessing`)\n",
"- [Job distribution via `dask`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.01-PyData-ddG-pssm.ipynb#Job-distribution-via-`dask`)\n",
"- [Analysis of delta score](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.01-PyData-ddG-pssm.ipynb#Analysis-of-delta-score)\n",
"* Links\n",
" - [Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation](https://doi.org/10.1002/pro.3721)\n",
"\n",
"### [16.2 Distributed computation example: miniprotein design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.02-PyData-miniprotein-design.ipynb)\n",
"* Links\n",
" - [Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation](https://doi.org/10.1002/pro.3721)\n",
"\n",
"### [16.3 Example of Using PyRosetta with GNU Parallel](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.03-GNU-Parallel-Via-Slurm.ipynb)\n",
" - [1. Parallelize script in an interactive session:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.03-GNU-Parallel-Via-Slurm.ipynb#1.-Parallelize-script-in-an-interactive-session:)\n",
" - [2. Parallelize script on a high-performance computing cluster with Slurm scheduling (non-interactive submission):](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.03-GNU-Parallel-Via-Slurm.ipynb#2.-Parallelize-script-on-a-high-performance-computing-cluster-with-Slurm-scheduling-(non-interactive-submission):)\n",
" - [3. Submit jobs individually to the SLURM scheduler:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.03-GNU-Parallel-Via-Slurm.ipynb#3.-Submit-jobs-individually-to-the-SLURM-scheduler:)\n",
"\n",
"### [16.4 Examples Using the `dask` Module](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.04-dask.delayed-Via-Slurm.ipynb)\n",
" - [We can make use of the `dask` library to parallelize code](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.04-dask.delayed-Via-Slurm.ipynb#We-can-make-use-of-the-`dask`-library-to-parallelize-code)\n",
" - [Consider the following example that runs within this Jupyter notebook kernel just fine but could be parallelized:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.04-dask.delayed-Via-Slurm.ipynb#Consider-the-following-example-that-runs-within-this-Jupyter-notebook-kernel-just-fine-but-could-be-parallelized:)\n",
"\n",
"### [16.5 Part I: Parallelized Global Ligand Docking with `pyrosetta.distributed`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.05-Ligand-Docking-dask.ipynb)\n",
"\n",
"### [16.6 PyRosettaCluster Tutorial 1A. Simple protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb)\n",
" - [1. Import packages](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb#1.-Import-packages)\n",
" - [2. Initialize a compute cluster using `dask`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb#2.-Initialize-a-compute-cluster-using-`dask`)\n",
" - [3. Define or import the user-provided PyRosetta protocol(s):](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb#3.-Define-or-import-the-user-provided-PyRosetta-protocol(s):)\n",
" - [Let's look at the definition of the user-provided PyRosetta protocol `my_protocol` located in `additional_scripts/my_protocols.py`:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb#Let's-look-at-the-definition-of-the-user-provided-PyRosetta-protocol-`my_protocol`-located-in-`additional_scripts/my_protocols.py`:)\n",
" - [4. Define the user-provided keyword argument(s) (i.e. `kwargs`):](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb#4.-Define-the-user-provided-keyword-argument(s)-(i.e.-`kwargs`):)\n",
" - [5. Launch the original simulation using the `distribute()` method](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb#5.-Launch-the-original-simulation-using-the-`distribute()`-method)\n",
" - [7. Visualize the resultant decoy](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb#7.-Visualize-the-resultant-decoy)\n",
" - [Congrats!](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb#Congrats!)\n",
"* Figures\n",
" - [title](Media/dask_labextension_1.png)\n",
" - [title](Media/dask_labextension_2.png)\n",
" - [title](Media/dask_labextension_4.png)\n",
" - [title](Media/dask_labextension_3.png)\n",
" - [title](Media/viewer_1.png)\n",
"* Links\n",
" - [documentation](https://www.rosettacommons.org/docs/latest/rosetta_basics/options/run-options)\n",
"\n",
"### [16.7 PyRosettaCluster Tutorial 1B. Reproduce simple protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb)\n",
" - [1. Import packages](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#1.-Import-packages)\n",
" - [2. Initialize a compute cluster using `dask`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#2.-Initialize-a-compute-cluster-using-`dask`)\n",
" - [3. Re-define or import the original user-provided PyRosetta protocol:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#3.-Re-define-or-import-the-original-user-provided-PyRosetta-protocol:)\n",
" - [4. Reproduce the original decoy:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#4.-Reproduce-the-original-decoy:)\n",
" - [5. Launch the reproduction simulation using `reproduce()`:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#5.-Launch-the-reproduction-simulation-using-`reproduce()`:)\n",
" - [6. Visualize the reproduced decoy:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#6.-Visualize-the-reproduced-decoy:)\n",
" - [7. Optionally, perform sanity checks to confirm that the reproduced decoy is identical to the original decoy:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#7.-Optionally,-perform-sanity-checks-to-confirm-that-the-reproduced-decoy-is-identical-to-the-original-decoy:)\n",
" - [Assert that the sequences are identical:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#Assert-that-the-sequences-are-identical:)\n",
" - [Assert that the `total_score`s are identical:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#Assert-that-the-`total_score`s-are-identical:)\n",
" - [Assert that the C$_{\\alpha}$–C$_{\\alpha}$ root-mean-square deviation (RMSD) is `0.0` Å:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#Assert-that-the-C$_{\\alpha}$–C$_{\\alpha}$-root-mean-square-deviation-(RMSD)-is-`0.0`-Å:)\n",
" - [Congrats!](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb#Congrats!)\n",
"\n",
"### [16.8 PyRosettaCluster Tutorial 2. Multiple protocols](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb)\n",
" - [1. Import packages](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb#1.-Import-packages)\n",
" - [2. Initialize a compute cluster using `dask`:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb#2.-Initialize-a-compute-cluster-using-`dask`:)\n",
" - [3. Define the user-provided PyRosetta protocols:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb#3.-Define-the-user-provided-PyRosetta-protocols:)\n",
" - [4. Define the user-provided kwargs:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb#4.-Define-the-user-provided-kwargs:)\n",
" - [5. Launch the original simulation using `distribute()`:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb#5.-Launch-the-original-simulation-using-`distribute()`:)\n",
" - [6. Visualize the resultant decoy:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb#6.-Visualize-the-resultant-decoy:)\n",
" - [Congrats!](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb#Congrats!)\n",
"\n",
"### [16.9 PyRosettaCluster Tutorial 3. Multiple decoys](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb)\n",
" - [1. Import packages](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb#1.-Import-packages)\n",
" - [2. Initialize a compute cluster using `dask`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb#2.-Initialize-a-compute-cluster-using-`dask`)\n",
" - [3. Define the user-provided PyRosetta protocols that returns multiple `Pose` or `PackedPose` objects:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb#3.-Define-the-user-provided-PyRosetta-protocols-that-returns-multiple-`Pose`-or-`PackedPose`-objects:)\n",
" - [4. Define the user-provided tasks as `kwargs`:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb#4.-Define-the-user-provided-tasks-as-`kwargs`:)\n",
" - [5. Launch the original simulation using `distribute()`:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb#5.-Launch-the-original-simulation-using-`distribute()`:)\n",
" - [6. Visualize the resulting decoys:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb#6.-Visualize-the-resulting-decoys:)\n",
" - [Congrats!](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb#Congrats!)\n",
"\n",
"### [16.10 PyRosettaCluster Tutorial 4. Ligand params](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb)\n",
" - [1. Import packages](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb#1.-Import-packages)\n",
" - [2. Initialize a compute cluster using `dask`:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb#2.-Initialize-a-compute-cluster-using-`dask`:)\n",
" - [3. Define ligand `.params` file(s) and initialize PyRosetta with a constant seed:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb#3.-Define-ligand-`.params`-file(s)-and-initialize-PyRosetta-with-a-constant-seed:)\n",
" - [4. Define the user-provided PyRosetta protocol:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb#4.-Define-the-user-provided-PyRosetta-protocol:)\n",
" - [5. Launch the original simulation using `distribute()`:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb#5.-Launch-the-original-simulation-using-`distribute()`:)\n",
" - [6. Visualize the resultant decoy:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb#6.-Visualize-the-resultant-decoy:)\n",
" - [Congrats!](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb#Congrats!)\n",
"\n",
"\n",
"## [Appendix A. Command Reference](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/A.00-Appendix-A.ipynb)\n",
"\n",
"\n",
"## [Appendix B. Residue Parameter Files](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/B.00-Appendix-B.ipynb)\n",
"\n",
"\n",
"## [Appendix C. Cleaning pdb files](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/C.00-Appendix-C.ipynb)\n",
"\n",
"\n",
"## [Appendix D. Links to Online Help](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/D.00-Appendix-D.ipynb)"
]
}
],
"metadata": {},
"nbformat": 4,
"nbformat_minor": 5
}