{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "Before you turn this problem in, make sure everything runs as expected. First, **restart the kernel** (in the menubar, select Kernel$\\rightarrow$Restart) and then **run all cells** (in the menubar, select Cell$\\rightarrow$Run All).\n", "\n", "Make sure you fill in any place that says `YOUR CODE HERE` or \"YOUR ANSWER HERE\", as well as your name and collaborators below:" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "NAME = \"\"\n", "COLLABORATORS = \"\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "---" ] }, { "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", "< [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb) >

\"Open" ] }, { "cell_type": "markdown", "metadata": { "deletable": false, "editable": false, "nbgrader": { "checksum": "6aa8f28ae9ee095a08190784a96bdd18", "grade": false, "grade_id": "cell-c32668370dae07d5", "locked": true, "schema_version": 1, "solution": false } }, "source": [ "# Practice: Analyzing energy between residues\n", "Keywords: pose_from_rcsb(), pdb2pose(), EMapVector()" ] }, { "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": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# From previous section:\n", "sfxn = get_score_function(True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Analyze the energy between residues Y102 and Q408 in cetuximab (PDB code 1YY9, use the `pyrosetta.toolbox.pose_from_rcsb` function to download it and load it into a new `Pose` object) by following the steps below. \n", "\n", "A. Internally, a Pose object has a list of residues, numbered starting from 1. To find the residue numbers of Y102 of chain D and Q408 of chain A, use the residue chain identifier and the PDB residue number to convert to the pose numbering using the `pose2pdb()` method:\n", "\n", "```\n", "pose = pyrosetta.toolbox.pose_from_rcsb(\"1YY9\")\n", "res102 = pose.pdb_info().pdb2pose(\"D\", 102)\n", "res408 = pose.pdb_info().pdb2pose(\"A\", 408)\n", "```" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# get the pose numbers for Y102 (chain D) and Q408 (chain A)" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "deletable": false, "nbgrader": { "checksum": "021521771cae846244b7da6fe1e5fbfe", "grade": true, "grade_id": "cell-870a6043eeeae1de", "locked": false, "points": 0, "schema_version": 1, "solution": true } }, "outputs": [], "source": [ "# YOUR CODE HERE\n", "raise NotImplementedError()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "B. Score the pose and determine the van der Waals energies and solvation energy between these two residues. Use the following commands to isolate contributions from particular pairs of residues, where `rsd102` and `rsd408` are the two residue objects of interest from above (not the residue number -- use `pose.residue(res_num)` to access the objects): \n", "\n", "```\n", "emap = EMapVector()\n", "sfxn.eval_ci_2b(pose.residue(res102), pose.residue(res408), pose, emap)\n", "print(emap[fa_atr])\n", "print(emap[fa_rep])\n", "print(emap[fa_sol])\n", "```" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "code_folding": [], "deletable": false, "nbgrader": { "checksum": "c7eb996bd82c409aba707dab13c6e707", "grade": true, "grade_id": "cell-1ffc5699ad9c088b", "locked": false, "points": 0, "schema_version": 1, "solution": true } }, "outputs": [], "source": [ "# YOUR CODE HERE\n", "raise NotImplementedError()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb) >

\"Open" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.0" }, "toc": { "base_numbering": 1, "nav_menu": {}, "number_sections": true, "sideBar": true, "skip_h1_title": false, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": {}, "toc_section_display": true, "toc_window_display": true } }, "nbformat": 4, "nbformat_minor": 2 }