notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb

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   "cell_type": "markdown",
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   "source": [
    "<!--NOTEBOOK_HEADER-->\n",
    "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta);\n",
    "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!--NAVIGATION-->\n",
    "< [Packing & Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.00-Introduction-to-Packing-and-Design.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.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": [
    "# Side Chain Conformations and Dunbrack Energies\n",
    "Keywords: phi(), psi(), energies(), residue_total_energies()\n",
    "\n",
    "# References\n",
    "1. Original Rotamer paper\n",
    "2. New rotamer paper\n",
    "\n",
    "# Recommended Resources\n",
    "1. Rotamer Library Homepage: http://dunbrack.fccc.edu/bbdep2010/\n",
    "2. Rotamer Library Interactive Overview: http://dunbrack.fccc.edu/bbdep2010/ImagesMovies.php"
   ]
  },
  {
   "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!\")\n",
    "\n",
    "from pyrosetta import *\n",
    "from pyrosetta.teaching import *\n",
    "init()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Begin by moving to the directory with your pdb files and loading cetuximab from 1YY8.clean.pdb used in previous workshops.\n",
    "\n",
    "```\n",
    "cd google_drive/My\\ Drive/student-notebooks/\n",
    "pose = pose_from_pdb(\"1YY8.clean.pdb\")\n",
    "start_pose = Pose()\n",
    "start_pose.assign(pose)\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mcore.init: \u001b[0mChecking for fconfig files in pwd and ./rosetta/flags\n",
      "\u001b[0mcore.init: \u001b[0mRosetta version: PyRosetta4.Release.python36.mac r208 2019.04+release.fd666910a5e fd666910a5edac957383b32b3b4c9d10020f34c1 http://www.pyrosetta.org 2019-01-22T15:55:37\n",
      "\u001b[0mcore.init: \u001b[0mcommand: PyRosetta -ex1 -ex2aro -database /Users/kathyle/Computational Protein Prediction and Design/PyRosetta4.Release.python36.mac.release-208/pyrosetta/database\n",
      "\u001b[0mcore.init: \u001b[0m'RNG device' seed mode, using '/dev/urandom', seed=-202618888 seed_offset=0 real_seed=-202618888\n",
      "\u001b[0mcore.init.random: \u001b[0mRandomGenerator:init: Normal mode, seed=-202618888 RG_type=mt19937\n",
      "\u001b[0mcore.chemical.GlobalResidueTypeSet: \u001b[0mFinished initializing fa_standard residue type set.  Created 696 residue types\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/kathyle/Computational Protein Prediction and Design/PyRosetta4.Release.python36.mac.release-208/pyrosetta/teaching.py:13: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.\n",
      "  from rosetta.core.scoring import *\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mcore.chemical.GlobalResidueTypeSet: \u001b[0mTotal time to initialize 1.13131 seconds.\n",
      "\u001b[0mcore.import_pose.import_pose: \u001b[0mFile '1YY8.clean.pdb' automatically determined to be of type PDB\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  CG  on residue ARG 18\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  CD  on residue ARG 18\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  NE  on residue ARG 18\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  CZ  on residue ARG 18\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  NH1 on residue ARG 18\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  NH2 on residue ARG 18\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  CG  on residue GLN:NtermProteinFull 214\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  CD  on residue GLN:NtermProteinFull 214\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  OE1 on residue GLN:NtermProteinFull 214\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0m\u001b[1m[ WARNING ]\u001b[0m missing heavyatom:  NE2 on residue GLN:NtermProteinFull 214\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 23 88\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 23 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 88 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 23 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 88 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 134 194\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 134 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 194 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 134 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 194 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 235 308\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 235 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 308 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 235 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 308 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mFound disulfide between residues 359 415\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 359 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 415 CYS\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 359 CYD\n",
      "\u001b[0mcore.conformation.Conformation: \u001b[0mcurrent variant for 415 CYD\n",
      "\u001b[0mcore.pack.pack_missing_sidechains: \u001b[0mpacking residue number 18 because of missing atom number 6 atom name  CG\n",
      "\u001b[0mcore.pack.pack_missing_sidechains: \u001b[0mpacking residue number 214 because of missing atom number 6 atom name  CG\n",
      "\u001b[0mcore.pack.task: \u001b[0mPacker task: initialize from command line()\n",
      "\u001b[0mcore.scoring.ScoreFunctionFactory: \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n",
      "\u001b[0mcore.scoring.etable: \u001b[0mStarting energy table calculation\n",
      "\u001b[0mcore.scoring.etable: \u001b[0msmooth_etable: changing atr/rep split to bottom of energy well\n",
      "\u001b[0mcore.scoring.etable: \u001b[0msmooth_etable: spline smoothing lj etables (maxdis = 6)\n",
      "\u001b[0mcore.scoring.etable: \u001b[0msmooth_etable: spline smoothing solvation etables (max_dis = 6)\n",
      "\u001b[0mcore.scoring.etable: \u001b[0mFinished calculating energy tables.\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/rama/fd/all.ramaProb\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/rama/fd/prepro.ramaProb\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.all.txt\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/P_AA\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/P_AA_n\n",
      "\u001b[0mcore.scoring.P_AA: \u001b[0mshapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\n",
      "\u001b[0mbasic.io.database: \u001b[0mDatabase file opened: scoring/score_functions/elec_cp_reps.dat\n",
      "\u001b[0mcore.scoring.elec.util: \u001b[0mRead 40 countpair representative atoms\n",
      "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mshapovalov_lib_fixes_enable option is true.\n",
      "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mshapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\n",
      "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mBinary rotamer library selected: /Users/kathyle/Computational Protein Prediction and Design/PyRosetta4.Release.python36.mac.release-208/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\n",
      "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mUsing Dunbrack library binary file '/Users/kathyle/Computational Protein Prediction and Design/PyRosetta4.Release.python36.mac.release-208/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\n",
      "\u001b[0mcore.pack.dunbrack.RotamerLibrary: \u001b[0mDunbrack 2010 library took 0.386455 seconds to load from binary\n",
      "\u001b[0mcore.pack.pack_rotamers: \u001b[0mbuilt 43 rotamers at 2 positions.\n",
      "\u001b[0mcore.pack.interaction_graph.interaction_graph_factory: \u001b[0mInstantiating DensePDInteractionGraph\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<pyrosetta.rosetta.core.pose.Pose at 0x1066dc0a0>"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pose = pose_from_pdb(\"inputs/1YY8.clean.pdb\")\n",
    "start_pose = Pose()\n",
    "start_pose.assign(pose)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "__Question:__ What are the φ, ψ, and χ angles of residue K49?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LYS\n",
      "Phi: -122.41752\n",
      "Psi: 153.08267\n",
      "\n",
      "Chi 1: 68.12458\n",
      "Chi 2: -169.18576\n",
      "Chi 3: -175.37028\n",
      "Chi 4: -169.58806\n"
     ]
    }
   ],
   "source": [
    "print(pose.residue(49).name())\n",
    "print(\"Phi: %.5f\\nPsi: %.5f\\n\" %(pose.phi(49), pose.psi(49)))\n",
    "print(\"Chi 1: %.5f\\nChi 2: %.5f\\nChi 3: %.5f\\nChi 4: %.5f\" %(pose.chi(1, 49), pose.chi(2, 49), pose.chi(3, 49), pose.chi(4, 49)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Score your pose with the standard full-atom score function. What is the energy of K49? Note the Dunbrack energy component (`fa_dun`), which represents the side-chain conformational probability given phi/psi (Ie backbone-dependant). \n",
    "\n",
    "Any energy can be converted to a probability.  Use this energy (E) to calculate the approximate probability of the rotamer (p): p=e^(-E)\n",
    "```\n",
    "scorefxn = get_fa_scorefxn()\n",
    "scorefxn(pose)\n",
    "energies = pose.energies()\n",
    "print(energies.residue_total_energies(49))\n",
    "print(energies.residue_total_energies(49)[pyrosetta.rosetta.core.scoring.fa_dun])\n",
    "```"
   ]
  },
  {
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     "grade_id": "cell-f210fdda6b087d77",
     "locked": false,
     "points": 0,
     "schema_version": 1,
     "solution": true
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0mcore.scoring.ScoreFunctionFactory: \u001b[0mSCOREFUNCTION: \u001b[32mref2015\u001b[0m\n",
      "( fa_atr; -8.83354) ( fa_rep; 2.78019) ( fa_sol; 5.92847) ( fa_intra_atr; -1.68168) ( fa_intra_rep; 2.47533) ( fa_intra_sol; 1.20218) ( fa_intra_atr_xover4; -0.52776) ( fa_intra_rep_xover4; 0.191981) ( fa_intra_sol_xover4; 0.292855) ( fa_intra_atr_nonprotein; 0) ( fa_intra_rep_nonprotein; 0) ( fa_intra_sol_nonprotein; 0) ( fa_intra_RNA_base_phos_atr; 0) ( fa_intra_RNA_base_phos_rep; 0) ( fa_intra_RNA_base_phos_sol; 0) ( fa_atr_dummy; 0) ( fa_rep_dummy; 0) ( fa_sol_dummy; 0) ( fa_vdw_tinker; 0) ( lk_hack; 0) ( lk_ball; 0) ( lk_ball_wtd; 0.321463) ( lk_ball_iso; 0) ( lk_ball_bridge; 0) ( lk_ball_bridge_uncpl; 0) ( coarse_fa_atr; 0) ( coarse_fa_rep; 0) ( coarse_fa_sol; 0) ( coarse_beadlj; 0) ( mm_lj_intra_rep; 0) ( mm_lj_intra_atr; 0) ( mm_lj_inter_rep; 0) ( mm_lj_inter_atr; 0) ( mm_twist; 0) ( mm_bend; 0) ( mm_stretch; 0) ( lk_costheta; 0) ( lk_polar; 0) ( lk_nonpolar; 0) ( lk_polar_intra_RNA; 0) ( lk_nonpolar_intra_RNA; 0) ( fa_elec; -2.75782) ( fa_elec_bb_bb; 0) ( fa_elec_bb_sc; 0) ( fa_elec_sc_sc; 0) ( fa_intra_elec; 0) ( h2o_hbond; 0) ( dna_dr; 0) ( dna_bp; 0) ( dna_bs; 0) ( dna_ref; 0) ( peptide_bond; 0) ( pcs; 0) ( pcsTs1; 0) ( pcsTs2; 0) ( pcsTs3; 0) ( pcsTs4; 0) ( pcs2; 0) ( fastsaxs; 0) ( saxs_score; 0) ( saxs_cen_score; 0) ( saxs_fa_score; 0) ( pddf_score; 0) ( fiberdiffraction; 0) ( fiberdiffractiondens; 0) ( fa_mbenv; 0) ( fa_mbsolv; 0) ( fa_elec_rna_phos_phos; 0) ( fa_elec_rna_phos_sugr; 0) ( fa_elec_rna_phos_base; 0) ( fa_elec_rna_sugr_sugr; 0) ( fa_elec_rna_sugr_base; 0) ( fa_elec_rna_base_base; 0) ( fa_elec_rna_phos_phos_fast; 0) ( fa_elec_rna_phos_sugr_fast; 0) ( fa_elec_rna_phos_base_fast; 0) ( fa_elec_rna_sugr_sugr_fast; 0) ( fa_elec_rna_sugr_base_fast; 0) ( fa_elec_rna_base_base_fast; 0) ( fa_elec_aro_aro; 0) ( fa_elec_aro_all; 0) ( hack_aro; 0) ( rna_fa_atr_base; 0) ( rna_fa_rep_base; 0) ( rna_data_backbone; 0) ( ch_bond; 0) ( ch_bond_bb_bb; 0) ( ch_bond_sc_sc; 0) ( ch_bond_bb_sc; 0) ( pro_close; 0) ( rama2b; 0) ( vdw; 0) ( cenpack; 0) ( cenpack_smooth; 0) ( cen_hb; 0) ( hybrid_vdw; 0) ( gauss; 0) ( rna_vdw; 0) ( rnp_vdw; 0) ( rna_base_backbone; 0) ( rna_backbone_backbone; 0) ( rna_repulsive; 0) ( rna_base_pair_pairwise; 0) ( rna_base_axis_pairwise; 0) ( rna_base_stagger_pairwise; 0) ( rna_base_stack_pairwise; 0) ( rna_base_stack_axis_pairwise; 0) ( rna_data_base; 0) ( rna_base_pair; 0) ( rna_base_axis; 0) ( rna_base_stagger; 0) ( rna_base_stack; 0) ( rna_base_stack_axis; 0) ( rnp_base_pair; 0) ( rnp_stack; 0) ( rnp_stack_xy; 0) ( rnp_pair; 0) ( rnp_pair_dist; 0) ( rnp_aa_to_rna_backbone; 0) ( rna_mg_point; 0) ( rna_mg_point_indirect; 0) ( mg; 0) ( mg_lig; 0) ( mg_sol; 0) ( mg_ref; 0) ( hoh_ref; 0) ( rna_torsion; 0) ( rna_torsion_sc; 0) ( rna_suite; 0) ( rna_jr_suite; 0) ( suiteness_bonus; 0) ( tna_suite; 0) ( rna_sugar_close; 0) ( fa_stack; 0) ( fa_stack_lower; 0) ( fa_stack_upper; 0) ( fa_stack_aro; 0) ( fa_stack_ext; 0) ( fa_stack_sol; 0) ( fa_stack_lr; 0) ( fa_stack_rna_protein; 0) ( fa_stack_rna_protein_aro; 0) ( ss_contact_worst; 0) ( stack_elec; 0) ( stack_elec_base_base; 0) ( stack_elec_base_bb; 0) ( alignment; 0) ( dna_bb_torsion; 0) ( dna_sugar_close; 0) ( dna_base_distance; 0) ( geom_sol_fast; 0) ( geom_sol_fast_intra_RNA; 0) ( fa_cust_pair_dist; 0) ( custom_atom_pair; 0) ( orbitals_hpol_bb; 0) ( pci_cation_pi; 0) ( pci_pi_pi; 0) ( pci_salt_bridge; 0) ( pci_hbond; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_first; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_161; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_162; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_163; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_164; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_165; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_166; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_167; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_168; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_169; 0) ( PyRosettaTwoBodyContextIndepenedentEnergy_last; 0) ( python; 0) ( fa_pair; 0) ( fa_pair_aro_aro; 0) ( fa_pair_aro_pol; 0) ( fa_pair_pol_pol; 0) ( hbond_sr_bb; 0) ( hbond_lr_bb; 0) ( hbond_bb_sc; 0) ( hbond_sr_bb_sc; 0) ( hbond_lr_bb_sc; 0) ( hbond_sc; 0) ( hbond_intra; 0) ( hbond_wat; 0) ( wat_entropy; 0) ( hbond; 0) ( npd_hbond_sr_bb; 0) ( npd_hbond_lr_bb; 0) ( npd_hbond_bb_sc; 0) ( npd_hbond_sr_bb_sc; 0) ( npd_hbond_lr_bb_sc; 0) ( npd_hbond_sc; 0) ( npd_hbond_intra; 0) ( npd_hbond; 0) ( fa_grpelec; 0) ( PyRosettaTwoBodyContextDependentEnergy_first; 0) ( PyRosettaTwoBodyContextDependentEnergy_196; 0) ( PyRosettaTwoBodyContextDependentEnergy_197; 0) ( PyRosettaTwoBodyContextDependentEnergy_198; 0) ( PyRosettaTwoBodyContextDependentEnergy_199; 0) ( PyRosettaTwoBodyContextDependentEnergy_200; 0) ( PyRosettaTwoBodyContextDependentEnergy_201; 0) ( PyRosettaTwoBodyContextDependentEnergy_202; 0) ( PyRosettaTwoBodyContextDependentEnergy_203; 0) ( PyRosettaTwoBodyContextDependentEnergy_204; 0) ( PyRosettaTwoBodyContextDependentEnergy_last; 0) ( interface_dd_pair; 0) ( geom_sol; 0) ( geom_sol_intra_RNA; 0) ( occ_sol_fitted; 0) ( occ_sol_fitted_onebody; 0) ( occ_sol_exact; 0) ( cen_rot_pair; 0) ( cen_rot_pair_ang; 0) ( cen_rot_pair_dih; 0) ( pair; 0) ( cen_pair_smooth; 0) ( Mpair; 0) ( mp_pair; 0) ( fa_mpsolv; 0) ( suck; 0) ( rna_rg; 0) ( rna_motif; 0) ( facts_elec; 0) ( facts_solv; 0) ( facts_sasa; 0) ( motif_dock; 0) ( pointwater; 0) ( goap; 0) ( goap_dist; 0) ( goap_angle; 0) ( approximate_buried_unsat_penalty; 0) ( interchain_pair; 0) ( interchain_vdw; 0) ( gb_elec; 0) ( multipole_elec; 0) ( fa_sasa; 0) ( dslf_ss_dst; 0) ( dslf_cs_ang; 0) ( dslf_ss_dih; 0) ( dslf_ca_dih; 0) ( dslf_cbs_ds; 0) ( dslf_fa13; 0) ( dslfc_cen_dst; 0) ( dslfc_cb_dst; 0) ( dslfc_ang; 0) ( dslfc_cb_dih; 0) ( dslfc_bb_dih; 0) ( dslfc_rot; 0) ( dslfc_trans; 0) ( dslfc_RT; 0) ( atom_pair_constraint; 0) ( base_pair_constraint; 0) ( coarse_chainbreak_constraint; 0) ( constant_constraint; 0) ( coordinate_constraint; 0) ( angle_constraint; 0) ( dihedral_constraint; 0) ( big_bin_constraint; 0) ( dunbrack_constraint; 0) ( site_constraint; 0) ( metalhash_constraint; 0) ( metalbinding_constraint; 0) ( rna_stub_coord_hack; 0) ( bond_geometry; 0) ( rna_bond_geometry; 0) ( Hpol_bond_geometry; 0) ( rama; 0) ( omega; 0.0116849) ( fa_dun; 3.97212) ( fa_dun_dev; 1.07017) ( fa_dun_rot; 2.90195) ( fa_dun_semi; 0) ( cen_rot_dun; 0) ( dna_chi; 0) ( p_aa_pp; 0.0112208) ( p_aa_ss; 0) ( yhh_planarity; 0) ( hxl_tors; 0) ( h2o_intra; 0) ( ref; -0.71458) ( ref_nc; 0) ( seqdep_ref; 0) ( nmer_ref; 0) ( nmer_pssm; 0) ( nmer_svm; 0) ( envsmooth; 0) ( e_pH; 0) ( rna_bulge; 0) ( dna_dihedral_bb; 0) ( dna_dihedral_chi; 0) ( dna_dihedral_sugar; 0) ( sugar_bb; 0) ( free_suite; 0) ( free_2HOprime; 0) ( free_side_chain; 0) ( free_base; 0) ( free_res; 0) ( free_dof; 0) ( intermol; 0) ( other_pose; 0) ( special_rot; 0) ( PB_elec; 0) ( cen_env_smooth; 0) ( cbeta_smooth; 0) ( cen_rot_env; 0) ( cen_rot_cbeta; 0) ( env; 0) ( cbeta; 0) ( DFIRE; 0) ( Menv; 0) ( Mcbeta; 0) ( Menv_non_helix; 0) ( Menv_termini; 0) ( Menv_tm_proj; 0) ( Mlipo; 0) ( rg; 0) ( rg_local; 0) ( co; 0) ( hs_pair; 0) ( ss_pair; 0) ( rsigma; 0) ( sheet; 0) ( burial_v2; 0) ( burial; 0) ( abego; 0) ( hrf_ms_labeling; 0) ( rnp_env; 0) ( loop_close; 0) ( missing_res; 0) ( mp_env; 0) ( mp_cbeta; 0) ( mp_lipo; 0) ( mp_termini; 0) ( mp_nonhelix; 0) ( mp_tmproj; 0) ( fa_mpenv; 0) ( fa_mpenv_smooth; 0) ( mp_res_lipo; 0) ( span_ins; 0) ( mp_span_ang; 0) ( mp_helicality; 0) ( natbias_ss; 0) ( natbias_hs; 0) ( natbias_hh; 0) ( natbias_stwist; 0) ( aa_cmp; 0) ( dock_ens_conf; 0) ( csa; 0) ( dc; 0) ( rdc; 0) ( rdc_segments; 0) ( rdc_rohl; 0) ( nmr_pcs; 0) ( nmr_rdc; 0) ( nmr_pre; 0) ( cen_pair_motifs; 0) ( cen_pair_motif_degree; 0) ( holes; 0) ( holes_decoy; 0) ( holes_resl; 0) ( holes_min; 0) ( holes_min_mean; 0) ( rna_chem_shift; 0) ( rna_chem_map; 0) ( rna_chem_map_lores; 0) ( rna_partition; 0) ( dab_sasa; 0) ( dab_sev; 0) ( sa; 0) ( d2h_sa; 0) ( ProQM; 0) ( ProQ; 0) ( interchain_env; 0) ( interchain_contact; 0) ( chainbreak; 0) ( linear_chainbreak; 0) ( overlap_chainbreak; 0) ( distance_chainbreak; 0) ( dof_constraint; 0) ( branch_conn; 0) ( linear_branch_conn; 0) ( rama_prepro; -0.0498918) ( paa_abego3; 0) ( cart_bonded; 0) ( cart_bonded_angle; 0) ( cart_bonded_length; 0) ( cart_bonded_ring; 0) ( cart_bonded_torsion; 0) ( cart_bonded_proper; 0) ( cart_bonded_improper; 0) ( gen_bonded; 0) ( gen_bonded_bond; 0) ( gen_bonded_angle; 0) ( gen_bonded_torsion; 0) ( gen_bonded_improper; 0) ( neigh_vect; 0) ( neigh_count; 0) ( neigh_vect_raw; 0) ( symE_bonus; 0) ( sym_lig; 0) ( mhc_epitope; 0) ( pack_stat; 0) ( rms_energy; 0) ( res_type_constraint; 0) ( res_type_linking_constraint; 0) ( pocket_constraint; 0) ( backbone_stub_constraint; 0) ( backbone_stub_linear_constraint; 0) ( surface; 0) ( p_aa; 0) ( unfolded; 0) ( split_unfolded_two_body; 0) ( fa_atr_ref; 0) ( fa_rep_ref; 0) ( fa_sol_ref; 0) ( fa_elec_ref; 0) ( hbond_ref; 0) ( dslf_fa13_ref; 0) ( fa_intra_atr_ref; 0) ( fa_intra_rep_ref; 0) ( fa_intra_sol_ref; 0) ( pro_close_ref; 0) ( fa_dun_ref; 0) ( fa_dun_dev_ref; 0) ( fa_dun_rot_ref; 0) ( fa_dun_semi_ref; 0) ( rama_ref; 0) ( p_aa_pp_ref; 0) ( omega_ref; 0) ( mm_lj_intra_rep_ref; 0) ( mm_lj_intra_atr_ref; 0) ( mm_twist_ref; 0) ( elec_dens_fast; 0) ( elec_dens_window; 0) ( elec_dens_whole_structure_ca; 0) ( elec_dens_whole_structure_allatom; 0) ( elec_dens_atomwise; 0) ( grid_vdw; 0) ( xtal_ml; 0) ( xtal_rwork; 0) ( xtal_rfree; 0) ( hpatch; 0) ( Menv_smooth; 0) ( wat_desolv; 0) ( ring_close; 0) ( aa_repeat; 0) ( aa_composition; 0) ( aspartimide_penalty; 0) ( hbnet; 0) ( buried_unsatisfied_penalty; 0) ( netcharge; 0) ( voids_penalty; 0) ( dna_env; 0) ( dna_pair; 0) ( dump_trajectory; 0) ( PyRosettaEnergy_first; 0) ( PyRosettaEnergy_457; 0) ( PyRosettaEnergy_458; 0) ( PyRosettaEnergy_459; 0) ( PyRosettaEnergy_460; 0) ( PyRosettaEnergy_461; 0) ( PyRosettaEnergy_462; 0) ( PyRosettaEnergy_463; 0) ( PyRosettaEnergy_464; 0) ( PyRosettaEnergy_465; 0) ( PyRosettaEnergy_last; 0) ( sidechain_neighbors; 0) ( membrane_span_constraint; 0) ( membrane_span_term_z_constraint; 0) ( total_score; -1.45222) ( dummy_score_type; 0) \n",
      "3.972124341964819\n"
     ]
    }
   ],
   "source": [
    "### BEGIN SOLUTION\n",
    "scorefxn = get_fa_scorefxn()\n",
    "scorefxn(pose)\n",
    "energies = pose.energies()\n",
    "print(energies.residue_total_energies(49))\n",
    "print(energies.residue_total_energies(49)[pyrosetta.rosetta.core.scoring.fa_dun])\n",
    "### END SOLUTION"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use `pose.set_chi(<i>, <res_num>, <chi>)` to set the side chain of residue 49 to the all-anti conformation. (Here, `i` is the χ index, and `chi` is the new torsion angle in degrees.) Re-score the pose and note the Dunbrack energy."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
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     "grade": true,
     "grade_id": "cell-74a711eb920136be",
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     "solution": true
    }
   },
   "outputs": [],
   "source": [
    "for i in range(1, 5):\n",
    "    pose.set_chi(i, 49, 180)\n",
    "    \n",
    "### BEGIN SOLUTION\n",
    "scorefxn(pose)\n",
    "print(energies.residue_total_energies(49))\n",
    "print(energies.residue_total_energies(49)[pyrosetta.rosetta.core.scoring.fa_dun])\n",
    "### END SOLUTION"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<!--NAVIGATION-->\n",
    "< [Packing & Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.00-Introduction-to-Packing-and-Design.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb) ><p><a href=\"https://colab.research.google.com/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.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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