notebooks/10.00-Working-With-Symmetry.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!--NOTEBOOK_HEADER-->\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": [
    "<!--NAVIGATION-->\n",
    "< [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>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Working With Symmetry\n",
    "Keywords: symmetry, asymmetric, SetupForSymmetryMover, virtual\n",
    "\n",
    "## Overview\n",
    "Symmetry is an important concept to learn when working with biomolecules.  When a protein is crystalized, it is in the precense of its symmetrical neighbors - which can be important if testing particular protocols or using crystal density for refinement or full structure building.\n",
    "\n",
    "Symmetry can also be useful for designing symmetrical structures or large repeating meta-proteins like protein cages. \n",
    "\n",
    "### Symmetry In Rosetta\n",
    "So why do we care if our protein is symmetrical or not when it comes to Rosetta?  Each residue and atom that is loaded into Rosetta takes time to both load, and time to score.  Since scoring can happen thousands of times - even in a short protocol, anything we can do to speed this up becomes important. The most expensive operation in Rosetta is minimization, and by using symmetry - we can reduce the minimization time exponentially by minimizing a single copy instead of ALL copies.  We will get into the details about how this works below.\n",
    "\n",
    "When we use symmetry in Rosetta - we are basically telling rosetta that the symmetrical partners are 'special', however, the total number of residues is now ALL residues, including symmetrical partners.  Upon setting up symmety in Rosetta, Rosetta will replace the `Conformation` within the pose with a **Symmetrical** version, called the `SymmetricConformation`.  If you know anything about classes, this `SymmetricConformation` is derived from the actual `Conformation` object, but contains extra information about the pose and some functions are replaced. \n",
    "\n",
    "### Symmetric Scoring and Moving\n",
    "Ok, so now lets assume that we have our symmetric pose.  Now what?  Well, the symmetric copies are all tied to their real counterparts.  Once you move a chain, residue, or atom by packing or minimization, the symmetric copies of that residue are all moved in the same way. \n",
    "\n",
    "Cool.  But what about scoring?  Scoring works very similarly - instead of scoring each and every residue in our pose, Rosetta will score just our assymetric unit, and multiply that out to the number of symmetric copies we have.  Intelligently, Rosetta will also figure out the symmetric interfaces that arise from the interactions of our assymetric unit to the symmetric copies and score them appropriately.\n",
    "\n",
    "### Symmetry-aware movers\n",
    "Most of our common movers are symmetry-aware.  At one point there were different symmetric and non-symmetric versions of particular code, such as MinMover and PackRotamersMover.  Now though, Rosetta will automatically use the pose to figure out what needs to be done. You should seek original documentation (and contact the author if not explicit) to make sure that an uncommon protocol you are using is symmetry-aware.\n",
    "\n",
    "## Documentation\n",
    "More information on RosettaSymmetry can be found in the following places:\n",
    "- https://www.rosettacommons.org/docs/latest/rosetta_basics/structural_concepts/symmetry\n",
    "- https://www.rosettacommons.org/demos/latest/tutorials/Symmetry/Symmetry\n",
    "- https://www.rosettacommons.org/docs/latest/application_documentation/utilities/make-symmdef-file\n",
    "- https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/SetupForSymmetryMover\n",
    "- https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/ExtractAsymmetricUnitMover\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Notebook setup\n",
    "import sys\n",
    "if 'google.colab' in sys.modules:\n",
    "    !pip install pyrosettacolabsetup\n",
    "    import pyrosettacolabsetup\n",
    "    pyrosettacolabsetup.setup()\n",
    "    print (\"Notebook is set for PyRosetta use in Colab.  Have fun!\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here, we will use a few specific options. The first three options make Rosetta a bit more robust to input structures.  The `-load_PDB_components` cannot be used with glycans, unfortunately, and our structure has a few very important glycans.  Finally, we load a bunch of glycan-specific options, which we will cover in the next tutorial."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "PyRosetta-4 2019 [Rosetta PyRosetta4.Release.python36.mac 2019.39+release.93456a567a8125cafdf7f8cb44400bc20b570d81 2019-09-26T14:24:44] retrieved from: http://www.pyrosetta.org\n",
      "(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n",
      "\u001b[0mcore.init: \u001b[0mChecking for fconfig files in pwd and ./rosetta/flags\n",
      "\u001b[0mcore.init: \u001b[0mReading fconfig.../Users/jadolfbr/.rosetta/flags/common\n",
      "\u001b[0mcore.init: \u001b[0m\n",
      "\u001b[0mcore.init: \u001b[0m\n",
      "\u001b[0mcore.init: \u001b[0mRosetta version: PyRosetta4.Release.python36.mac r233 2019.39+release.93456a567a8 93456a567a8125cafdf7f8cb44400bc20b570d81 http://www.pyrosetta.org 2019-09-26T14:24:44\n",
      "\u001b[0mcore.init: \u001b[0mcommand: PyRosetta -ignore_unrecognized_res -load_PDB_components false -ignore_zero_occupancy false @inputs/glycan_flags -database /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database\n",
      "\u001b[0mbasic.random.init_random_generator: \u001b[0m'RNG device' seed mode, using '/dev/urandom', seed=1544006277 seed_offset=0 real_seed=1544006277\n",
      "\u001b[0mbasic.random.init_random_generator: \u001b[0mRandomGenerator:init: Normal mode, seed=1544006277 RG_type=mt19937\n"
     ]
    }
   ],
   "source": [
    "from pyrosetta import *\n",
    "from pyrosetta.rosetta import *\n",
    "from pyrosetta.teaching import *\n",
    "import os\n",
    "\n",
    "init('-ignore_unrecognized_res -load_PDB_components false -ignore_zero_occupancy false @inputs/glycan_flags')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creating a SymDef file\n",
    "\n",
    "Here, we will start with how to create a basic symdef file for cyrstal symmetry.  Note that there are ways to do this without a symdef file, but these do not currently work for glycan structures, which we will be using here. \n",
    "\n",
    "The `make_symdef_file.pl` file is within Rosetta3. To use it, you will need to download and licence Rosetta3.  The code is in the `Rosetta/main/src/apps/public` directory. In the interest of reducing code drift, this file is NOT included in the tutorial directory as we may then have version drift.  \n",
    "\n",
    "If you have done this, we can use the following command to create the symdef file.  Here, the radius of symmetrical partners is 12A, which is certainly fairly large, but produces a very well represented crystal."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cd inputs && make_symmdef_file.pl -r 12 -m CRYST -p  inputs/1jnd.pdb.pdb > inputs/1jnd.pdb_crys.symm && cd -\n"
     ]
    }
   ],
   "source": [
    "pdb = \"inputs/1jnd.pdb\"\n",
    "base_cmd = f'cd inputs && make_symmdef_file.pl -r 12 -m CRYST -p  {pdb}.pdb > {pdb}_crys.symm && cd -'\n",
    "print(base_cmd)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use this base command and the `os.system(cmd)` function to run the code or use the provided symdef file. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "os.system('cp inputs/1jnd_crys.symm .')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Take a look at the symmetrized structure in pymol (`inputs/1jnd_symm.pdb`).  What would happen if we increased the radius to 24 instead of 12?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup a Symmetrized Pose\n",
    "\n",
    "Here, we will run a basic Rosetta protocol with symmetry.  There are much more complicated things you can do with symmetry, but for now, we just want to symmetrically pack the protein.  Please see the docs for more on symmetry.  The full Rosetta C++ tutorial for symmetry is a great place to go from here: - https://www.rosettacommons.org/demos/latest/tutorials/Symmetry/Symmetry \n",
    "\n",
    "Lets first create a pose, and then use the `SetupForSymmetryMover` on the pose. Note this is an unrefined input structure.  This is so that minmover will actually do something.  A pareto-optimal refined structure can be found in the inputs as `1jnd_refined.pdb.gz`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mcore.import_pose.import_pose: \u001b[0mFile 'inputs/1jnd.pdb' automatically determined to be of type PDB\n",
      "\u001b[0mcore.io.pdb.pdb_reader: \u001b[0mParsing 82 .pdb records with unknown format to search for Rosetta-specific comments.\n",
      "\u001b[0mcore.io.util: \u001b[0mAutomatic glycan connection is activated.\n",
      "\u001b[0mcore.io.util: \u001b[0mStart reordering residues.\n",
      "\u001b[0mcore.io.util: \u001b[0mCorrected glycan residue order (internal numbering): [401, 402, 403, 404]\n",
      "\u001b[0mcore.io.util: \u001b[0m\n",
      "\u001b[0mcore.io.pose_from_sfr.PoseFromSFRBuilder: \u001b[0mSetting chain termination for 404\n",
      "\u001b[0mcore.io.pose_from_sfr.PoseFromSFRBuilder: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Glc401 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\n",
      "\u001b[0mcore.io.pose_from_sfr.PoseFromSFRBuilder: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Glc402 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\n",
      "\u001b[0mcore.io.pose_from_sfr.PoseFromSFRBuilder: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Man403 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\n",
      "\u001b[0mcore.io.pose_from_sfr.PoseFromSFRBuilder: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Man404 has an unfavorable ring conformation; the coordinates for this input structure may have been poorly assigned.\n",
      "\u001b[0mcore.chemical.AtomICoor: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 401.  Returning BOGUS ID instead.\n",
      "\u001b[0mcore.conformation.Residue: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing an atom: 401  H1  that depends on a nonexistent polymer connection!\n",
      "\u001b[0mcore.conformation.Residue: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m  --> generating it using idealized coordinates.\n",
      "\u001b[0mcore.chemical.AtomICoor: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue ->4)-beta-D-Glcp:2-AcNH 401.  Returning BOGUS ID instead.\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 5 32\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 5 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 32 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 5 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 32 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 302 385\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 302 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 385 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 302 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 385 CYD\n",
      "\u001b[0mcore.conformation.carbohydrates.GlycanTreeSet: \u001b[0mSetting up Glycan Trees\n",
      "\u001b[0mcore.conformation.carbohydrates.GlycanTreeSet: \u001b[0mFound 1 glycan trees.\n"
     ]
    }
   ],
   "source": [
    "p = pose_from_pdb('inputs/1jnd.pdb')\n",
    "original = p.clone()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "404"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p.total_residue()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "pyrosetta.rosetta.core.conformation.Conformation"
      ]
     },
     "execution_count": 39,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(p.conformation())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Setting weight of master jump ( jump-id=1 ) to 1.0 (was undefined)\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Setting jump_group JUMPGROUP1: [master 1]  6:0  7:0  2:0  3:0  4:0  5:0  8:0  9:0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Setting weight of master jump ( jump-id=10 ) to 1.0 (was undefined)\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m Setting jump_group JUMPGROUP2: [master 10]  20:0  22:0  12:0  14:0  16:0  18:0  24:0  26:0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0msymmetry name: 1jnd_P_32_2_1\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mnumber of subunits: 9\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mnumber of interfaces: 1\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mscore subunit number: VRT_0_0_0_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0manchor the subunits at residue: 1\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_0_0_0_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: 1 0 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: 0 1 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 73.8756 49.0221 11.025\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_0_0_0_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: 1 0 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: 0 1 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 72.8756 48.0221 10.025\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_1_1_0_n1\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0.866025 -0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 26.9528 39.4671 -18.9707\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_1_1_0_n1_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0.866025 -0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 28.3188 39.1011 -19.9707\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_2_1_1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 -0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: 0.866025 -0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 58.6891 3.60826 41.0206\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_2_1_1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 -0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: 0.866025 -0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 58.3231 4.97428 40.0206\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_3_0_n1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: 0.866025 0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 58.6891 -3.60826 -11.025\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_3_0_n1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: 0.866025 0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 58.3231 -4.97428 -10.025\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_3_1_0_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: 0.866025 0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 111.862 88.4892 -11.025\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_3_1_0_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: 0.866025 0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 111.496 87.1232 -10.025\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_4_2_1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 -0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0.866025 0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 80.1253 52.6304 48.9664\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_4_2_1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 -0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0.866025 0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 81.4913 52.9964 49.9664\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_4_2_1_n1\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 -0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0.866025 0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 80.1253 52.6304 -41.0206\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_4_2_1_n1_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: -0.5 -0.866025 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0.866025 0.5 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 81.4913 52.9964 -40.0206\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_5_0_1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: 1 0 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0 -1 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 20.7031 43.0754 18.9707\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_5_0_1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: 1 0 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0 -1 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 19.7031 44.0754 19.9707\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_5_1_1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: 1 0 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0 -1 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 127.048 43.0754 18.9707\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0m Virtual coordinate system VRT_5_1_1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx: 1 0 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my: -0 -1 0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0morigin: 126.048 44.0754 19.9707\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mDof for jump: 1\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx 0:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my 0:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mz 0:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx_angle 1:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my_angle 1:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mz_angle 1:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mDof for jump: 10\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx 1:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my 1:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mz 1:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mx_angle 0:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0my_angle 0:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mz_angle 0:0,0:0,0 n2c\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_0_0_0_0_to_com VRT_0_0_0_0 VRT_0_0_0_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_0_0_0_0_to_subunit VRT_0_0_0_0_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_1_1_0_n1 VRT_0_0_0_0 VRT_1_1_0_n1\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_1_1_0_n1_to_com VRT_1_1_0_n1 VRT_1_1_0_n1_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_1_1_0_n1_to_subunit VRT_1_1_0_n1_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_2_1_1_0 VRT_0_0_0_0 VRT_2_1_1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_2_1_1_0_to_com VRT_2_1_1_0 VRT_2_1_1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_2_1_1_0_to_subunit VRT_2_1_1_0_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_3_0_n1_0 VRT_0_0_0_0 VRT_3_0_n1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_3_0_n1_0_to_com VRT_3_0_n1_0 VRT_3_0_n1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_3_0_n1_0_to_subunit VRT_3_0_n1_0_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_3_1_0_0 VRT_0_0_0_0 VRT_3_1_0_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_3_1_0_0_to_com VRT_3_1_0_0 VRT_3_1_0_0_base\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_3_1_0_0_to_subunit VRT_3_1_0_0_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_4_2_1_0 VRT_0_0_0_0 VRT_4_2_1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_4_2_1_0_to_com VRT_4_2_1_0 VRT_4_2_1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_4_2_1_0_to_subunit VRT_4_2_1_0_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_4_2_1_n1 VRT_0_0_0_0 VRT_4_2_1_n1\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_4_2_1_n1_to_com VRT_4_2_1_n1 VRT_4_2_1_n1_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_4_2_1_n1_to_subunit VRT_4_2_1_n1_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_5_0_1_0 VRT_0_0_0_0 VRT_5_0_1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_5_0_1_0_to_com VRT_5_0_1_0 VRT_5_0_1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_5_0_1_0_to_subunit VRT_5_0_1_0_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_5_1_1_0 VRT_0_0_0_0 VRT_5_1_1_0\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_5_1_1_0_to_com VRT_5_1_1_0 VRT_5_1_1_0_base\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mJump JUMP_5_1_1_0_to_subunit VRT_5_1_1_0_base SUBUNIT\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mInclude subunit:\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mOutput subunit:\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mSlideType: RANDOM\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mSlideCriteriaType: CEN_DOCK_SCORE\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mSlideCriteriaVal: AUTOMATIC\n",
      "\u001b[0mcore.conformation.symmetry.SymmData: \u001b[0mSlideOrder: none\n",
      "\u001b[0mcore.conformation.symmetry.util: \u001b[0m=================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================\n",
      "VRT_0_0_0_0(3637)\n",
      "|----#j10#--->VRT_0_0_0_0_base(3638)----#j1#------>1:Sub1A(1-400)\n",
      "|----=j11=--->VRT_1_1_0_n1(3643)---j12=10--->VRT_1_1_0_n1_base(3644)----j2=1---->1213:Sub4A(1213-1612)\n",
      "|----=j13=--->VRT_2_1_1_0(3645)---j14=10--->VRT_2_1_1_0_base(3646)----j3=1---->1617:Sub5A(1617-2016)\n",
      "|----=j15=--->VRT_3_0_n1_0(3647)---j16=10--->VRT_3_0_n1_0_base(3648)----j4=1---->2021:Sub6A(2021-2420)\n",
      "|----=j17=--->VRT_3_1_0_0(3649)---j18=10--->VRT_3_1_0_0_base(3650)----j5=1---->2425:Sub7A(2425-2824)\n",
      "|----=j19=--->VRT_4_2_1_0(3639)---j20=10--->VRT_4_2_1_0_base(3640)----j6=1---->405:Sub2A(405-804)\n",
      "|----=j21=--->VRT_4_2_1_n1(3641)---j22=10--->VRT_4_2_1_n1_base(3642)----j7=1---->809:Sub3A(809-1208)\n",
      "|----=j23=--->VRT_5_0_1_0(3651)---j24=10--->VRT_5_0_1_0_base(3652)----j8=1---->2829:Sub8A(2829-3228)\n",
      "\\----=j25=--->VRT_5_1_1_0(3653)---j26=10--->VRT_5_1_1_0_base(3654)----j9=1---->3233:Sub9A(3233-3632)\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mFound disulfide between residues 5 32\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 5 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 32 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 5 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 32 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 409 to 436\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 813 to 840\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1217 to 1244\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1621 to 1648\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2025 to 2052\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2429 to 2456\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2833 to 2860\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 3237 to 3264\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 5 to 32\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mFound disulfide between residues 302 385\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 302 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 385 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 302 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 385 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 706 to 789\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1110 to 1193\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1514 to 1597\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1918 to 2001\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2322 to 2405\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2726 to 2809\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 3130 to 3213\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 3534 to 3617\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 302 to 385\n",
      "\u001b[0mcore.conformation.carbohydrates.GlycanTreeSet: \u001b[0mSetting up Glycan Trees\n",
      "\u001b[0mcore.conformation.carbohydrates.GlycanTreeSet: \u001b[0mFound 9 glycan trees.\n",
      "\u001b[0mprotocols.simple_moves_symmetry.SymDockingInitialPerturbation: \u001b[0mReading options...\n"
     ]
    }
   ],
   "source": [
    "symmetrize = rosetta.protocols.symmetry.SetupForSymmetryMover(\"1jnd_crys.symm\")\n",
    "symmetrize.apply(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3654\n",
      "<class 'pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation'>\n"
     ]
    }
   ],
   "source": [
    "print(p.total_residue())\n",
    "print(type(p.conformation()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "How many symmetric copies do we have in our pose?\n",
    "How do the scores compare for our original pose and our symmetrized version?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now lets use some of the functionality to understand how this all works. We can use the `SymetricInfo` object that is part of the `SymmetricConformation` to get at some info. Lets take a look at all residues and find the assymetric unit residues and equivalent residues for the rest."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "AssymUnit? equivalent_res\n",
      "1 True 0\n",
      "2 True 0\n",
      "3 True 0\n",
      "4 True 0\n",
      "5 True 0\n",
      "6 True 0\n",
      "7 True 0\n",
      "8 True 0\n",
      "9 True 0\n",
      "10 True 0\n",
      "11 True 0\n",
      "12 True 0\n",
      "13 True 0\n",
      "14 True 0\n",
      "15 True 0\n",
      "16 True 0\n",
      "17 True 0\n",
      "18 True 0\n",
      "19 True 0\n",
      "20 True 0\n",
      "21 True 0\n",
      "22 True 0\n",
      "23 True 0\n",
      "24 True 0\n",
      "25 True 0\n",
      "26 True 0\n",
      "27 True 0\n",
      "28 True 0\n",
      "29 True 0\n",
      "30 True 0\n",
      "31 True 0\n",
      "32 True 0\n",
      "33 True 0\n",
      "34 True 0\n",
      "35 True 0\n",
      "36 True 0\n",
      "37 True 0\n",
      "38 True 0\n",
      "39 True 0\n",
      "40 True 0\n",
      "41 True 0\n",
      "42 True 0\n",
      "43 True 0\n",
      "44 True 0\n",
      "45 True 0\n",
      "46 True 0\n",
      "47 True 0\n",
      "48 True 0\n",
      "49 True 0\n",
      "50 True 0\n",
      "51 True 0\n",
      "52 True 0\n",
      "53 True 0\n",
      "54 True 0\n",
      "55 True 0\n",
      "56 True 0\n",
      "57 True 0\n",
      "58 True 0\n",
      "59 True 0\n",
      "60 True 0\n",
      "61 True 0\n",
      "62 True 0\n",
      "63 True 0\n",
      "64 True 0\n",
      "65 True 0\n",
      "66 True 0\n",
      "67 True 0\n",
      "68 True 0\n",
      "69 True 0\n",
      "70 True 0\n",
      "71 True 0\n",
      "72 True 0\n",
      "73 True 0\n",
      "74 True 0\n",
      "75 True 0\n",
      "76 True 0\n",
      "77 True 0\n",
      "78 True 0\n",
      "79 True 0\n",
      "80 True 0\n",
      "81 True 0\n",
      "82 True 0\n",
      "83 True 0\n",
      "84 True 0\n",
      "85 True 0\n",
      "86 True 0\n",
      "87 True 0\n",
      "88 True 0\n",
      "89 True 0\n",
      "90 True 0\n",
      "91 True 0\n",
      "92 True 0\n",
      "93 True 0\n",
      "94 True 0\n",
      "95 True 0\n",
      "96 True 0\n",
      "97 True 0\n",
      "98 True 0\n",
      "99 True 0\n",
      "100 True 0\n",
      "101 True 0\n",
      "102 True 0\n",
      "103 True 0\n",
      "104 True 0\n",
      "105 True 0\n",
      "106 True 0\n",
      "107 True 0\n",
      "108 True 0\n",
      "109 True 0\n",
      "110 True 0\n",
      "111 True 0\n",
      "112 True 0\n",
      "113 True 0\n",
      "114 True 0\n",
      "115 True 0\n",
      "116 True 0\n",
      "117 True 0\n",
      "118 True 0\n",
      "119 True 0\n",
      "120 True 0\n",
      "121 True 0\n",
      "122 True 0\n",
      "123 True 0\n",
      "124 True 0\n",
      "125 True 0\n",
      "126 True 0\n",
      "127 True 0\n",
      "128 True 0\n",
      "129 True 0\n",
      "130 True 0\n",
      "131 True 0\n",
      "132 True 0\n",
      "133 True 0\n",
      "134 True 0\n",
      "135 True 0\n",
      "136 True 0\n",
      "137 True 0\n",
      "138 True 0\n",
      "139 True 0\n",
      "140 True 0\n",
      "141 True 0\n",
      "142 True 0\n",
      "143 True 0\n",
      "144 True 0\n",
      "145 True 0\n",
      "146 True 0\n",
      "147 True 0\n",
      "148 True 0\n",
      "149 True 0\n",
      "150 True 0\n",
      "151 True 0\n",
      "152 True 0\n",
      "153 True 0\n",
      "154 True 0\n",
      "155 True 0\n",
      "156 True 0\n",
      "157 True 0\n",
      "158 True 0\n",
      "159 True 0\n",
      "160 True 0\n",
      "161 True 0\n",
      "162 True 0\n",
      "163 True 0\n",
      "164 True 0\n",
      "165 True 0\n",
      "166 True 0\n",
      "167 True 0\n",
      "168 True 0\n",
      "169 True 0\n",
      "170 True 0\n",
      "171 True 0\n",
      "172 True 0\n",
      "173 True 0\n",
      "174 True 0\n",
      "175 True 0\n",
      "176 True 0\n",
      "177 True 0\n",
      "178 True 0\n",
      "179 True 0\n",
      "180 True 0\n",
      "181 True 0\n",
      "182 True 0\n",
      "183 True 0\n",
      "184 True 0\n",
      "185 True 0\n",
      "186 True 0\n",
      "187 True 0\n",
      "188 True 0\n",
      "189 True 0\n",
      "190 True 0\n",
      "191 True 0\n",
      "192 True 0\n",
      "193 True 0\n",
      "194 True 0\n",
      "195 True 0\n",
      "196 True 0\n",
      "197 True 0\n",
      "198 True 0\n",
      "199 True 0\n",
      "200 True 0\n",
      "201 True 0\n",
      "202 True 0\n",
      "203 True 0\n",
      "204 True 0\n",
      "205 True 0\n",
      "206 True 0\n",
      "207 True 0\n",
      "208 True 0\n",
      "209 True 0\n",
      "210 True 0\n",
      "211 True 0\n",
      "212 True 0\n",
      "213 True 0\n",
      "214 True 0\n",
      "215 True 0\n",
      "216 True 0\n",
      "217 True 0\n",
      "218 True 0\n",
      "219 True 0\n",
      "220 True 0\n",
      "221 True 0\n",
      "222 True 0\n",
      "223 True 0\n",
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      "1934 False 318\n",
      "1935 False 319\n",
      "1936 False 320\n",
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      "1939 False 323\n",
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      "1944 False 328\n",
      "1945 False 329\n",
      "1946 False 330\n",
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      "1949 False 333\n",
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      "1957 False 341\n",
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      "1969 False 353\n",
      "1970 False 354\n",
      "1971 False 355\n",
      "1972 False 356\n",
      "1973 False 357\n",
      "1974 False 358\n",
      "1975 False 359\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1976 False 360\n",
      "1977 False 361\n",
      "1978 False 362\n",
      "1979 False 363\n",
      "1980 False 364\n",
      "1981 False 365\n",
      "1982 False 366\n",
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      "1992 False 376\n",
      "1993 False 377\n",
      "1994 False 378\n",
      "1995 False 379\n",
      "1996 False 380\n",
      "1997 False 381\n",
      "1998 False 382\n",
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      "2000 False 384\n",
      "2001 False 385\n",
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      "2013 False 397\n",
      "2014 False 398\n",
      "2015 False 399\n",
      "2016 False 400\n",
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      "2515 False 91\n",
      "2516 False 92\n",
      "2517 False 93\n",
      "2518 False 94\n",
      "2519 False 95\n",
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    {
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     "output_type": "stream",
     "text": [
      "2882 False 54\n",
      "2883 False 55\n",
      "2884 False 56\n",
      "2885 False 57\n",
      "2886 False 58\n",
      "2887 False 59\n",
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      "3252 False 20\n",
      "3253 False 21\n",
      "3254 False 22\n",
      "3255 False 23\n",
      "3256 False 24\n",
      "3257 False 25\n",
      "3258 False 26\n",
      "3259 False 27\n",
      "3260 False 28\n",
      "3261 False 29\n",
      "3262 False 30\n",
      "3263 False 31\n",
      "3264 False 32\n",
      "3265 False 33\n",
      "3266 False 34\n",
      "3267 False 35\n",
      "3268 False 36\n",
      "3269 False 37\n",
      "3270 False 38\n",
      "3271 False 39\n",
      "3272 False 40\n",
      "3273 False 41\n",
      "3274 False 42\n",
      "3275 False 43\n",
      "3276 False 44\n",
      "3277 False 45\n",
      "3278 False 46\n",
      "3279 False 47\n",
      "3280 False 48\n",
      "3281 False 49\n",
      "3282 False 50\n",
      "3283 False 51\n",
      "3284 False 52\n",
      "3285 False 53\n",
      "3286 False 54\n",
      "3287 False 55\n",
      "3288 False 56\n",
      "3289 False 57\n",
      "3290 False 58\n",
      "3291 False 59\n",
      "3292 False 60\n",
      "3293 False 61\n",
      "3294 False 62\n",
      "3295 False 63\n",
      "3296 False 64\n",
      "3297 False 65\n",
      "3298 False 66\n",
      "3299 False 67\n",
      "3300 False 68\n",
      "3301 False 69\n",
      "3302 False 70\n",
      "3303 False 71\n",
      "3304 False 72\n",
      "3305 False 73\n",
      "3306 False 74\n",
      "3307 False 75\n",
      "3308 False 76\n",
      "3309 False 77\n",
      "3310 False 78\n",
      "3311 False 79\n",
      "3312 False 80\n",
      "3313 False 81\n",
      "3314 False 82\n",
      "3315 False 83\n",
      "3316 False 84\n",
      "3317 False 85\n",
      "3318 False 86\n",
      "3319 False 87\n",
      "3320 False 88\n",
      "3321 False 89\n",
      "3322 False 90\n",
      "3323 False 91\n",
      "3324 False 92\n",
      "3325 False 93\n",
      "3326 False 94\n",
      "3327 False 95\n",
      "3328 False 96\n",
      "3329 False 97\n",
      "3330 False 98\n",
      "3331 False 99\n",
      "3332 False 100\n",
      "3333 False 101\n",
      "3334 False 102\n",
      "3335 False 103\n",
      "3336 False 104\n",
      "3337 False 105\n",
      "3338 False 106\n",
      "3339 False 107\n",
      "3340 False 108\n",
      "3341 False 109\n",
      "3342 False 110\n",
      "3343 False 111\n",
      "3344 False 112\n",
      "3345 False 113\n",
      "3346 False 114\n",
      "3347 False 115\n",
      "3348 False 116\n",
      "3349 False 117\n",
      "3350 False 118\n",
      "3351 False 119\n",
      "3352 False 120\n",
      "3353 False 121\n",
      "3354 False 122\n",
      "3355 False 123\n",
      "3356 False 124\n",
      "3357 False 125\n",
      "3358 False 126\n",
      "3359 False 127\n",
      "3360 False 128\n",
      "3361 False 129\n",
      "3362 False 130\n",
      "3363 False 131\n",
      "3364 False 132\n",
      "3365 False 133\n",
      "3366 False 134\n",
      "3367 False 135\n",
      "3368 False 136\n",
      "3369 False 137\n",
      "3370 False 138\n",
      "3371 False 139\n",
      "3372 False 140\n",
      "3373 False 141\n",
      "3374 False 142\n",
      "3375 False 143\n",
      "3376 False 144\n",
      "3377 False 145\n",
      "3378 False 146\n",
      "3379 False 147\n",
      "3380 False 148\n",
      "3381 False 149\n",
      "3382 False 150\n",
      "3383 False 151\n",
      "3384 False 152\n",
      "3385 False 153\n",
      "3386 False 154\n",
      "3387 False 155\n",
      "3388 False 156\n",
      "3389 False 157\n",
      "3390 False 158\n",
      "3391 False 159\n",
      "3392 False 160\n",
      "3393 False 161\n",
      "3394 False 162\n",
      "3395 False 163\n",
      "3396 False 164\n",
      "3397 False 165\n",
      "3398 False 166\n",
      "3399 False 167\n",
      "3400 False 168\n",
      "3401 False 169\n",
      "3402 False 170\n",
      "3403 False 171\n",
      "3404 False 172\n",
      "3405 False 173\n",
      "3406 False 174\n",
      "3407 False 175\n",
      "3408 False 176\n",
      "3409 False 177\n",
      "3410 False 178\n",
      "3411 False 179\n",
      "3412 False 180\n",
      "3413 False 181\n",
      "3414 False 182\n",
      "3415 False 183\n",
      "3416 False 184\n",
      "3417 False 185\n",
      "3418 False 186\n",
      "3419 False 187\n",
      "3420 False 188\n",
      "3421 False 189\n",
      "3422 False 190\n",
      "3423 False 191\n",
      "3424 False 192\n",
      "3425 False 193\n",
      "3426 False 194\n",
      "3427 False 195\n",
      "3428 False 196\n",
      "3429 False 197\n",
      "3430 False 198\n",
      "3431 False 199\n",
      "3432 False 200\n",
      "3433 False 201\n",
      "3434 False 202\n",
      "3435 False 203\n",
      "3436 False 204\n",
      "3437 False 205\n",
      "3438 False 206\n",
      "3439 False 207\n",
      "3440 False 208\n",
      "3441 False 209\n",
      "3442 False 210\n",
      "3443 False 211\n",
      "3444 False 212\n",
      "3445 False 213\n",
      "3446 False 214\n",
      "3447 False 215\n",
      "3448 False 216\n",
      "3449 False 217\n",
      "3450 False 218\n",
      "3451 False 219\n",
      "3452 False 220\n",
      "3453 False 221\n",
      "3454 False 222\n",
      "3455 False 223\n",
      "3456 False 224\n",
      "3457 False 225\n",
      "3458 False 226\n",
      "3459 False 227\n",
      "3460 False 228\n",
      "3461 False 229\n",
      "3462 False 230\n",
      "3463 False 231\n",
      "3464 False 232\n",
      "3465 False 233\n",
      "3466 False 234\n",
      "3467 False 235\n",
      "3468 False 236\n",
      "3469 False 237\n",
      "3470 False 238\n",
      "3471 False 239\n",
      "3472 False 240\n",
      "3473 False 241\n",
      "3474 False 242\n",
      "3475 False 243\n",
      "3476 False 244\n",
      "3477 False 245\n",
      "3478 False 246\n",
      "3479 False 247\n",
      "3480 False 248\n",
      "3481 False 249\n",
      "3482 False 250\n",
      "3483 False 251\n",
      "3484 False 252\n",
      "3485 False 253\n",
      "3486 False 254\n",
      "3487 False 255\n",
      "3488 False 256\n",
      "3489 False 257\n",
      "3490 False 258\n",
      "3491 False 259\n",
      "3492 False 260\n",
      "3493 False 261\n",
      "3494 False 262\n",
      "3495 False 263\n",
      "3496 False 264\n",
      "3497 False 265\n",
      "3498 False 266\n",
      "3499 False 267\n",
      "3500 False 268\n",
      "3501 False 269\n",
      "3502 False 270\n",
      "3503 False 271\n",
      "3504 False 272\n",
      "3505 False 273\n",
      "3506 False 274\n",
      "3507 False 275\n",
      "3508 False 276\n",
      "3509 False 277\n",
      "3510 False 278\n",
      "3511 False 279\n",
      "3512 False 280\n",
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      "3514 False 282\n",
      "3515 False 283\n",
      "3516 False 284\n",
      "3517 False 285\n",
      "3518 False 286\n",
      "3519 False 287\n",
      "3520 False 288\n",
      "3521 False 289\n",
      "3522 False 290\n",
      "3523 False 291\n",
      "3524 False 292\n",
      "3525 False 293\n",
      "3526 False 294\n",
      "3527 False 295\n",
      "3528 False 296\n",
      "3529 False 297\n",
      "3530 False 298\n",
      "3531 False 299\n",
      "3532 False 300\n",
      "3533 False 301\n",
      "3534 False 302\n",
      "3535 False 303\n",
      "3536 False 304\n",
      "3537 False 305\n",
      "3538 False 306\n",
      "3539 False 307\n",
      "3540 False 308\n",
      "3541 False 309\n",
      "3542 False 310\n",
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      "3544 False 312\n",
      "3545 False 313\n",
      "3546 False 314\n",
      "3547 False 315\n",
      "3548 False 316\n",
      "3549 False 317\n",
      "3550 False 318\n",
      "3551 False 319\n",
      "3552 False 320\n",
      "3553 False 321\n",
      "3554 False 322\n",
      "3555 False 323\n",
      "3556 False 324\n",
      "3557 False 325\n",
      "3558 False 326\n",
      "3559 False 327\n",
      "3560 False 328\n",
      "3561 False 329\n",
      "3562 False 330\n",
      "3563 False 331\n",
      "3564 False 332\n",
      "3565 False 333\n",
      "3566 False 334\n",
      "3567 False 335\n",
      "3568 False 336\n",
      "3569 False 337\n",
      "3570 False 338\n",
      "3571 False 339\n",
      "3572 False 340\n",
      "3573 False 341\n",
      "3574 False 342\n",
      "3575 False 343\n",
      "3576 False 344\n",
      "3577 False 345\n",
      "3578 False 346\n",
      "3579 False 347\n",
      "3580 False 348\n",
      "3581 False 349\n",
      "3582 False 350\n",
      "3583 False 351\n",
      "3584 False 352\n",
      "3585 False 353\n",
      "3586 False 354\n",
      "3587 False 355\n",
      "3588 False 356\n",
      "3589 False 357\n",
      "3590 False 358\n",
      "3591 False 359\n",
      "3592 False 360\n",
      "3593 False 361\n",
      "3594 False 362\n",
      "3595 False 363\n",
      "3596 False 364\n",
      "3597 False 365\n",
      "3598 False 366\n",
      "3599 False 367\n",
      "3600 False 368\n",
      "3601 False 369\n",
      "3602 False 370\n",
      "3603 False 371\n",
      "3604 False 372\n",
      "3605 False 373\n",
      "3606 False 374\n",
      "3607 False 375\n",
      "3608 False 376\n",
      "3609 False 377\n",
      "3610 False 378\n",
      "3611 False 379\n",
      "3612 False 380\n",
      "3613 False 381\n",
      "3614 False 382\n",
      "3615 False 383\n",
      "3616 False 384\n",
      "3617 False 385\n",
      "3618 False 386\n",
      "3619 False 387\n",
      "3620 False 388\n",
      "3621 False 389\n",
      "3622 False 390\n",
      "3623 False 391\n",
      "3624 False 392\n",
      "3625 False 393\n",
      "3626 False 394\n",
      "3627 False 395\n",
      "3628 False 396\n",
      "3629 False 397\n",
      "3630 False 398\n",
      "3631 False 399\n",
      "3632 False 400\n",
      "3633 False 401\n",
      "3634 False 402\n",
      "3635 False 403\n",
      "3636 False 404\n",
      "3637 True 0\n",
      "3638 True 0\n",
      "3639 True 0\n",
      "3640 True 0\n",
      "3641 True 0\n",
      "3642 True 0\n",
      "3643 True 0\n",
      "3644 True 0\n",
      "3645 True 0\n",
      "3646 True 0\n",
      "3647 True 0\n",
      "3648 True 0\n",
      "3649 True 0\n",
      "3650 True 0\n",
      "3651 True 0\n",
      "3652 True 0\n",
      "3653 True 0\n",
      "3654 True 0\n"
     ]
    }
   ],
   "source": [
    "print(\"AssymUnit? equivalent_res\")\n",
    "sym_info = p.conformation().Symmetry_Info()\n",
    "for i in range(1, p.size()+1):\n",
    "    print(i, sym_info.bb_is_independent(i), sym_info.bb_follows(i))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Which residues are our original pose residues?  Note that the final residues are called `Virtual` residues.  Virtual residues are not scored.  They have coordinates, and can move, but simply result in a score of zero.  They are useful in some contexts to hide a part of the pose from the scoring machinery, and there are movers that can change residues to and from virtual.  In this case, they are used for the FoldTree - in order to allow refinement of the full crystal environment.  They allow relative movement of each subunit relative to each other.  There are two virtual residues for each subunit"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Residue 3654: VRT (XXX, X):\n",
      "Base: VRT\n",
      " Properties: LIGAND VIRTUAL_RESIDUE\n",
      " Variant types:\n",
      " Main-chain atoms:\n",
      " Backbone atoms:  \n",
      " Side-chain atoms: ORIG  X    Y  \n",
      "Atom Coordinates:\n",
      "  ORIG: 126.048, 44.0754, 19.9707 (virtual)\n",
      "   X  : 127.048, 44.0754, 19.9707 (virtual)\n",
      "   Y  : 126.048, 43.0754, 19.9707 (virtual)\n",
      "Mirrored relative to coordinates in ResidueType: FALSE\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(p.residue(3654))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total Subunits: 9.0\n",
      "Total Subunits: 9\n"
     ]
    }
   ],
   "source": [
    "print(\"Total Subunits:\", (3654-18)/404)\n",
    "print(\"Total Subunits:\", sym_info.subunits())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mcore.scoring.ScoreFunctionFactory: \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n",
      "\u001b[0mcore.scoring.ScoreFunctionFactory: \u001b[0mThe -include_sugars flag was used with no sugar_bb weight set in the weights file.  Setting sugar_bb weight to 1.0 by default.\n",
      "-531.2534669946483\n",
      "-1132.7274634504747\n"
     ]
    }
   ],
   "source": [
    "score = get_score_function()\n",
    "print(score(original))\n",
    "print(score(p))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Running Protocols with Symmetry\n",
    "\n",
    "Now, lets try running a minimization with symmetry on.  "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [],
   "source": [
    "mm = MoveMap()\n",
    "mm.set_bb(True)\n",
    "mm.set_chi(True)\n",
    "minmover = rosetta.protocols.minimization_packing.MinMover()\n",
    "minmover.score_function(score)\n",
    "minmover.set_movemap(mm)\n",
    "if if not os.getenv(\"DEBUG\"):\n",
    "    minmover.apply(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-1147.371462425749"
      ]
     },
     "execution_count": 55,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "score(p)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "How does our pose look?  For being such a large pose, how was the speed of minimization? \n",
    "\n",
    "How does this compare to our refined pose?  Try to copy a subunit to a new object in PyMol.  Then use the align command to align it to our assymetric unit.  What is the RMSD?"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now lets pack with our symmetric structure. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mcore.conformation.symmetry.util: \u001b[0m=================== SYM FOLD TREE, jump notation: =symfixed= *indep* #symdof# jump[=follows] ========================\n",
      "VRT_0_0_0_0(3637)\n",
      "|----#j10#--->VRT_0_0_0_0_base(3638)----#j1#------>1:Sub1A(1-400)\n",
      "|----=j11=--->VRT_1_1_0_n1(3643)---j12=10--->VRT_1_1_0_n1_base(3644)----j2=1---->1213:Sub4A(1213-1612)\n",
      "|----=j13=--->VRT_2_1_1_0(3645)---j14=10--->VRT_2_1_1_0_base(3646)----j3=1---->1617:Sub5A(1617-2016)\n",
      "|----=j15=--->VRT_3_0_n1_0(3647)---j16=10--->VRT_3_0_n1_0_base(3648)----j4=1---->2021:Sub6A(2021-2420)\n",
      "|----=j17=--->VRT_3_1_0_0(3649)---j18=10--->VRT_3_1_0_0_base(3650)----j5=1---->2425:Sub7A(2425-2824)\n",
      "|----=j19=--->VRT_4_2_1_0(3639)---j20=10--->VRT_4_2_1_0_base(3640)----j6=1---->405:Sub2A(405-804)\n",
      "|----=j21=--->VRT_4_2_1_n1(3641)---j22=10--->VRT_4_2_1_n1_base(3642)----j7=1---->809:Sub3A(809-1208)\n",
      "|----=j23=--->VRT_5_0_1_0(3651)---j24=10--->VRT_5_0_1_0_base(3652)----j8=1---->2829:Sub8A(2829-3228)\n",
      "\\----=j25=--->VRT_5_1_1_0(3653)---j26=10--->VRT_5_1_1_0_base(3654)----j9=1---->3233:Sub9A(3233-3632)\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mFound disulfide between residues 5 32\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 5 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 32 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 5 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 32 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 409 to 436\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 813 to 840\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1217 to 1244\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1621 to 1648\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2025 to 2052\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2429 to 2456\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2833 to 2860\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 3237 to 3264\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 5 to 32\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mFound disulfide between residues 302 385\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 302 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 385 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 302 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mcurrent variant for 385 CYD\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 706 to 789\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1110 to 1193\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1514 to 1597\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 1918 to 2001\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2322 to 2405\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 2726 to 2809\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 3130 to 3213\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 3534 to 3617\n",
      "\u001b[0mcore.conformation.symmetry.Conformation: \u001b[0mAdd symmetric chemical bond 302 to 385\n",
      "\u001b[0mcore.conformation.carbohydrates.GlycanTreeSet: \u001b[0mSetting up Glycan Trees\n",
      "\u001b[0mcore.conformation.carbohydrates.GlycanTreeSet: \u001b[0mFound 9 glycan trees.\n",
      "\u001b[0mprotocols.simple_moves_symmetry.SymDockingInitialPerturbation: \u001b[0mReading options...\n"
     ]
    }
   ],
   "source": [
    "from rosetta.core.pack.task import *\n",
    "from rosetta.core.pack.task.operation import *\n",
    "\n",
    "packer = PackRotamersMover()\n",
    "tf = rosetta.core.pack.task.TaskFactory()\n",
    "\n",
    "tf.push_back(RestrictToRepacking())\n",
    "tf.push_back(IncludeCurrent())\n",
    "packer.task_factory(tf)\n",
    "\n",
    "p = original.clone()\n",
    "symmetrize.apply(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mprotocols.minimization_packing.PackRotamersMover: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m undefined ScoreFunction -- creating a default one\n",
      "\u001b[0mcore.scoring.ScoreFunctionFactory: \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n",
      "\u001b[0mcore.scoring.ScoreFunctionFactory: \u001b[0mThe -include_sugars flag was used with no sugar_bb weight set in the weights file.  Setting sugar_bb weight to 1.0 by default.\n",
      "\u001b[0mcore.pack.rotamer_set.RotamerSet_: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m including current in order to get at least 1 rotamer !!!!!! 180 ASN:N-glycosylated\n",
      "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 5259 rotamers at 404 positions.\n",
      "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n"
     ]
    }
   ],
   "source": [
    "if not os.getenv(\"DEBUG\"):\n",
    "    packer.apply(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "packed -1960.9189300248413\n"
     ]
    }
   ],
   "source": [
    "print(\"packed\", score(p))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Conclusions\n",
    "\n",
    "Symmetry is a useful tool in the Rosetta Library.  There are also selectors and movers that you may find useful, such as the `AsymmetricUnitSelector` in `rosetta.core.select.residue_selectors` and the `ExtractAsymmetricUnitMover`, which will give you back just the single subunit, without any asymetric partners, and the `ExtractAsymmetricPoseMover`, which will remove 'symmetry' information and give you back a pose with all the subunits. The later of these can be found by importing `rosetta.protocols.symmetry`.\n",
    "\n",
    "Note that not ALL protocols will respect symmetry - so please check the original documentation to see if symmetry is supported.  If you are unsure, please email the developer."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Chapter contributors:**\n",
    "\n",
    "- Jared Adolf-Bryfogle (Scripps; Institute for Protein Innovation)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!--NAVIGATION-->\n",
    "< [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>"
   ]
  }
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