0_analyze_pdb.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Analyzing PDB file\n",
    "- We need to analyze the pdb file in order to be able to make correct decision about the simulations"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "\n",
       "# MD simulations of H3-H4, tails truncated\n",
       "- AMBER14SB force field\n",
       "- 50 mM NaCl\n",
       "- box 2nm\n"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Folder set to:  h3-h4_tm\n",
      "Project name:  h3-h4_tm\n"
     ]
    }
   ],
   "source": [
    "#Libraries and main variables initialized\n",
    "import MDAnalysis as mda\n",
    "from MDAnalysis.analysis import align\n",
    "from MDAnalysis.analysis.rms import rmsd\n",
    "import numpy as np\n",
    "import urllib.request, json\n",
    "import os\n",
    "import re\n",
    "import nglview as nv\n",
    "from funcs import get_files_from_git\n",
    "from funcs import view_nucl\n",
    "from IPython.display import Markdown, display\n",
    "\n",
    "#Reloading funcs if changed\n",
    "from importlib import reload \n",
    "import funcs,config\n",
    "reload(funcs)\n",
    "reload(config)\n",
    "\n",
    "%matplotlib inline\n",
    "\n",
    "from IPython.display import Markdown, display\n",
    "from config import folder,descr,pname,ssh_host\n",
    "display(Markdown(descr))\n",
    "print(\"Folder set to: \",folder)\n",
    "print(\"Project name: \",pname)\n",
    "print(\"SSH host set to:\",ssh_host)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash --out output --err error\n",
    "#Get the PDB-file\n",
    "wget https://files.rcsb.org/view/1KX5.pdb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/opt/miniconda3/envs/moldyn/lib/python3.7/site-packages/MDAnalysis/topology/guessers.py:72: UserWarning: Failed to guess the mass for the following atom types: MN\n",
      "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "62a3a6487eb348acbff3fb23d7744f30",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#Let's have a look\n",
    "nucl=mda.Universe(\"1KX5.pdb\")\n",
    "nv.show_mdanalysis(nucl,gui=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Use these tools \n",
    "https://www.rcsb.org/pdb/static.do?p=software/software_links/analysis_and_verification.html"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Check occupancy and B-factors"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## See water molecules and ions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's analyze pK \n",
    "https://en.wikipedia.org/wiki/Henderson–Hasselbalch_equation\n",
    "pK>pH - residue is protonated\n",
    "pK<pH - residue is deprotonated\n",
    "pH=7.0 - neutral"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash \n",
    "mkdir -p tmp\n",
    "cd tmp\n",
    "propka31 ../1KX5.pdb\n",
    "#see tmp/1KX5.pka or output below"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Let's try foldX"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "cd tmp\n",
    "cp ../1KX5.pdb .\n",
    "ln -s `which foldx | xargs dirname`/rotabase.txt .\n",
    "foldx --command=RepairPDB --pdb=1KX5.pdb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python [conda env:moldyn]",
   "language": "python",
   "name": "conda-env-moldyn-py"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}