{ "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", "< [Ligand Refinement in PyRosetta (a.k.a. High-Resolution Local Docking) Using the `ligand.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.00-Ligand-Docking-PyRosetta.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [`GALigandDock` Protocol with `pyrosetta.distributed` Using the `beta_cart.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb) >
"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Global Ligand Docking using `XMLObjects` Using the `ref2015.wts` Scorefunction"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"*Warning*: This notebook uses `pyrosetta.distributed.viewer` code, which runs in `jupyter notebook` and might not run if you're using `jupyterlab`."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"*Note:* This Jupyter notebook requires the PyRosetta distributed layer. Please make sure to activate the `PyRosetta.notebooks` conda environment before running this notebook. The kernel is set to use this environment. "
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
""
],
"text/plain": [
" 5 rows × 22 columns You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: \n",
" \n",
"
\n",
"\n",
" \n",
" \n",
" \n",
" \n",
" dslf_fa13 \n",
" fa_atr \n",
" fa_dun \n",
" fa_elec \n",
" fa_intra_rep \n",
" fa_intra_sol_xover4 \n",
" fa_rep \n",
" fa_sol \n",
" hbond_bb_sc \n",
" hbond_lr_bb \n",
" ... \n",
" interfE \n",
" lk_ball_wtd \n",
" omega \n",
" p_aa_pp \n",
" pro_close \n",
" rama_prepro \n",
" ref \n",
" rmsd_chX \n",
" total_score \n",
" yhh_planarity \n",
" \n",
" \n",
" test_lig_XMLObjects_1.pdb \n",
" 0.0 \n",
" -2141.790247 \n",
" 2839.589602 \n",
" -505.303161 \n",
" 1549.888068 \n",
" 90.394684 \n",
" 1355.538397 \n",
" 1338.970707 \n",
" -52.121705 \n",
" -49.476625 \n",
" ... \n",
" -28.276440 \n",
" -50.974895 \n",
" 16.443889 \n",
" -84.493475 \n",
" 91.445419 \n",
" 117.822680 \n",
" 81.74634 \n",
" 0.631487 \n",
" 1456.971339 \n",
" 1.100056 \n",
" \n",
" \n",
" test_lig_XMLObjects_4.pdb \n",
" 0.0 \n",
" -2117.511239 \n",
" 3002.017883 \n",
" -484.395373 \n",
" 1575.126871 \n",
" 91.668637 \n",
" 1434.239151 \n",
" 1329.615403 \n",
" -48.468502 \n",
" -47.234071 \n",
" ... \n",
" -15.162686 \n",
" -49.593810 \n",
" -1.135463 \n",
" -85.518547 \n",
" 68.279343 \n",
" 118.636338 \n",
" 81.74634 \n",
" 11.435035 \n",
" 1628.146163 \n",
" 0.366937 \n",
" \n",
" \n",
" test_lig_XMLObjects_0.pdb \n",
" 0.0 \n",
" -2101.634782 \n",
" 2881.724947 \n",
" -484.021972 \n",
" 1552.937939 \n",
" 90.957571 \n",
" 1395.967000 \n",
" 1307.276630 \n",
" -48.113076 \n",
" -47.985689 \n",
" ... \n",
" -11.798166 \n",
" -48.713822 \n",
" -0.016234 \n",
" -86.665216 \n",
" 73.794018 \n",
" 111.035818 \n",
" 81.74634 \n",
" 18.723389 \n",
" 1519.846938 \n",
" 0.360842 \n",
" \n",
" \n",
" test_lig_XMLObjects_2.pdb \n",
" 0.0 \n",
" -2108.199196 \n",
" 2995.956828 \n",
" -483.697206 \n",
" 1572.754514 \n",
" 91.583322 \n",
" 1441.994818 \n",
" 1317.274987 \n",
" -47.207246 \n",
" -47.496493 \n",
" ... \n",
" -9.164489 \n",
" -48.398568 \n",
" 3.595816 \n",
" -82.205583 \n",
" 73.140703 \n",
" 122.270933 \n",
" 81.74634 \n",
" 13.237048 \n",
" 1642.356614 \n",
" 0.294935 \n",
" \n",
" \n",
" \n",
"test_lig_XMLObjects_3.pdb \n",
" 0.0 \n",
" -2114.363249 \n",
" 2941.806947 \n",
" -471.461845 \n",
" 1563.092110 \n",
" 90.772894 \n",
" 1426.594993 \n",
" 1318.093586 \n",
" -47.347564 \n",
" -48.064493 \n",
" ... \n",
" 2.542285 \n",
" -49.704318 \n",
" 4.201275 \n",
" -83.261999 \n",
" 68.786798 \n",
" 117.522522 \n",
" 81.74634 \n",
" 9.790556 \n",
" 1591.672471 \n",
" 0.122519 \n",
"
\n jupyter labextension install jupyterlab_3dmol
\n",
" jupyter labextension install jupyterlab_3dmol