{ "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", "< [Structure Refinement](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.00-Structure-Refinement.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Refinement Protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.02-Refinement-Protocol.ipynb) >
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"# High-Resolution Movers\n",
"Keywords: keep_history(), MoveMap, SmallMover(), ShearMover(), angle_max(), set_bb(), MinMover(), MonteCarlo(), boltzmann(), TrialMover(), SequenceMover(), RepeatMover()"
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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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"**Make sure you are in the directory with the pdb files:**\n",
"\n",
"`cd google_drive/MyDrive/student-notebooks/`"
]
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"In the last workshop, you encountered the `ClassicFragmentMover`, which inserts a short sequence of backbone torsion angles, and the `SwitchResidueTypeSetMover`, which doesn’t actually change the conformation of the pose but instead swaps out the residue types used.\n",
"\n",
"\n",
"In this workshop, we will introduce a variety of other `Movers`, particularly those used in high-resolution refinement (e.g., in Bradley’s 2005 paper).\n",
"\n",
"Before you start, load the cleaned cetuximab protein 1YY8 that we've worked with previously (but just one Fab fragment, chain A and B) and make a copy of the pose so we can compare later:\n",
"\n",
"```\n",
"start = pose_from_pdb(\"1YY8.clean.pdb\")\n",
"test = Pose()\n",
"test.assign(start)\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=-1427340416 seed_offset=0 real_seed=-1427340416\n",
"\u001b[0mcore.init.random: \u001b[0mRandomGenerator:init: Normal mode, seed=-1427340416 RG_type=mt19937\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.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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