chapter 9

README.md

@@ -62,6 +62,9 @@ Many of the workshops have been adapted from the book *The PyRosetta Interactive
 - [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)
 - [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)
 
+### [Chapter 9.0 Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb)
+- [9.1 Using Rosetta Gen KIC](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb)
+
 ### [Chapter 10.0 Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb)
 
 ### [Chapter 11.0 Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb)

notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb

@@ -14,7 +14,7 @@
    "metadata": {},
    "source": [
     "<!--NAVIGATION-->\n",
-    "< [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) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
+    "< [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) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
    ]
   },
   {
@@ -1906,7 +1906,7 @@
    "metadata": {},
    "source": [
     "<!--NAVIGATION-->\n",
-    "< [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) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
+    "< [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) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Loop Modeling](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.00-Loop-Modeling.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
    ]
   }
  ],

notebooks/10.00-Working-With-Symmetry.ipynb

@@ -14,7 +14,7 @@
    "metadata": {},
    "source": [
     "<!--NAVIGATION-->\n",
-    "< [`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) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
+    "< [Using Rosetta Gen KIC](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
    ]
   },
   {
@@ -4462,7 +4462,7 @@
    "metadata": {},
    "source": [
     "<!--NAVIGATION-->\n",
-    "< [`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) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
+    "< [Using Rosetta Gen KIC](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/09.01-Using-Gen-KIC.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb\"><img align=\"left\" src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open in Colab\" title=\"Open in Google Colaboratory\"></a>"
    ]
   }
  ],