{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);\n", "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [*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) >
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"# *De Novo* Parametric Backbone Design\n",
"\n",
"Keywords: Parametric, Bundle, BundleGridSampler, MakeBundle\n",
"\n",
"## Overview\n",
"\n",
"In this workshop, we will give examples for how to do Parametric Protein Design using the RosettaScripts interface to Rosetta written. The code you will be using from Rosetta was written by Vikram Mulligan. The BundleGridSampler and MakeBundle movers are available through code in PyRosetta, but because of the many number of options to it, it is a bit easier to work with these in XML. We will use this opportunity to do see how easy it is to run XML in PyRosetta, but we will cover the code-level interface as well in this workshop. \n",
"\n",
"This is some cool stuff. Enjoy. :)\n",
"\n",
"Please refer to the docs for more info.\n",
"\n",
"https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/Movers-RosettaScripts\n",
"\n",
"https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/MakeBundleMover\n",
"\n",
"https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/BundleGridSamplerMover"
]
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"*Warning*: This notebook uses `pyrosetta.distributed.viewer` code, which runs in `jupyter notebook` and might not run if you're using `jupyterlab`."
]
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"!pip install pyrosettacolabsetup\n",
"import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n",
"import pyrosetta; pyrosetta.init()\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Make sure you are in the directory with the pdb files:**\n",
"\n",
"`cd google_drive/MyDrive/student-notebooks/`"
]
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"execution_count": 1,
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