{ "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", "< [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) >
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"# 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"
]
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"!pip install pyrosettacolabsetup\n",
"import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n",
"import pyrosetta; pyrosetta.init()\n",
"from pyrosetta import *\n",
"from pyrosetta.teaching import *\n",
"init()"
]
},
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"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/MyDrive/student-notebooks/\n",
"pose = pose_from_pdb(\"1YY8.clean.pdb\")\n",
"start_pose = Pose()\n",
"start_pose.assign(pose)\n",
"```"
]
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"\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"
]
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"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"
]
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"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"
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