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  {
   "cell_type": "markdown",
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   "source": [
    "## Representations and Visualization"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`Molecule` objects can be visualized either in VMD or in NGL, a WebGL javascript molecule viewer that's integrated in the Notebook.\n",
    "\n",
    "By default, VMD is used as a viewer. If one wants to use NGL, run the following:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from htmd.config import config\n",
    "config(viewer='webgl')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### On-the-fly molecule visualization and interaction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2016-11-09 22:39:17,264 - htmd.molecule.molecule - INFO - Using local copy for 3PTB: /home/joao/maindisk/software/repos/Acellera/htmd/htmd/data/pdb/3ptb.pdb\n"
     ]
    }
   ],
   "source": [
    "mol = Molecule('3PTB') # reloading the molecule\n",
    "mol.view(gui=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "It is also possible to apply multiple representations to a `Molecule` as in VMD.\n",
    "\n",
    "Representations use the same names as in VMD, even when using the NGL viewer. Important parameters are: **style**, **color**, and **sel**.   "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### The \"quick\" or \"transient\" view"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use the `Molecule.view` method, specifying the representation as arguments. Use the `hold` parameter so that following `Molecule.view` calls can overlay. Otherwise, representations will be cleared on every call."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "mol.view(sel='protein', style='NewCartoon', color='Index', hold=True)\n",
    "mol.view(sel='resname BEN', style='Licorice', color=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### The \"explicit\" way: using `Molecule.reps`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "One directly manipulates elements in the `reps` property of `Molecule` objects, with the views being stored in that property."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "rep 0: sel='protein', style='NewCartoon', color='Index'\n",
      "rep 1: sel='resname BEN', style='Licorice', color='1'\n",
      "\n"
     ]
    }
   ],
   "source": [
    "mol.reps.remove()   # Clear representations\n",
    "mol.reps.add(sel='protein', style='NewCartoon', color='Index')\n",
    "mol.reps.add(sel='resname BEN', style='Licorice', color=1)\n",
    "print(mol.reps)     # Show list of representations (equivalent to mol.reps.list())\n",
    "mol.view()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Atom selection expressions work as in VMD"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The following shows the molecule without a 6 Å thick slab in the middle (−3 Å ≤ `x` ≤ +3 Å):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "mol.reps.remove() # in order to remove the previouly stored representations\n",
    "mol.view(sel='x*x>9')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Visualizing a trajectory"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`Molecule` provides wrapping and aligning functionality for working with MD trajectories and improving the visualization."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from htmd.home import home\n",
    "molTraj = Molecule(home(dataDir='dhfr') + '/dhfr.psf')\n",
    "molTraj.read(home(dataDir='dhfr') + '/dhfr.xtc')\n",
    "molTraj.view()"
   ]
  }
 ],
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