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    "# PyMOL part 2 (of 3)\n",
    ">Biochemistry laboratories - 201\n",
    ">\n",
    ">Jean-Yves Sgro -jsgro@wisc.edu\n",
    "\n",
    "Find **this document** at: http://go.wisc.edu/v9kvvx\n",
    "\n",
    "*Note*: To see as slides click on gift icon <span class=\"fa fa-gift fa-2x menu-icon\"></span> at the top right. To revert back to page view click on book icon <span class=\"fa fa-book fa-2x menu-icon\"></span> when on the first slide.\n"
   ]
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  {
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   "source": [
    "## Set-up\n",
    "\n",
    "- check your name on the attendees list\n",
    "- choose an iMac (or use your laptop)\n",
    "- login with your ***UW Net ID***"
   ]
  },
  {
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   "metadata": {
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   "source": [
    "# Today summary slides\n",
    "\n",
    "- 6 slides per page, color [PDF](https://biochem.wisc.edu/sites/default/files/facilities/bcrf/tutorials/pymol/part_2/pdbpymol-fall-2017-part_2lr.pdf)\n",
    "\n",
    "- All tutorial materials are at https://biochem.wisc.edu/bcrf/tutorials"
   ]
  },
  {
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   "source": [
    "## Finding PyMOL\n",
    "\n",
    "- Click on the \"Finder\"<img src=\"https://support.apple.com/library/content/dam/edam/applecare/images/en_US/osx/finder_icon_basic.png\" width=\"100\"> at the bottom right of the **\"Dock\"** on the bottom of the screen.\n",
    "- This will open a new window.\n",
    "- On the left click on **\"Applications\"**\n",
    "- In the alphabetical list choose **\"MacPyMOL\"** or **\"MacPyMOL.app\"** and double click. This will open PyMOL on your screen.\n"
   ]
  },
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   "source": [
    "## PyMOL book: section for part 2 (of 3)\n",
    "- start on page **79**\n",
    "- end on page **106**\n",
    "\n",
    "> This book is a **loaner** with a number marked on it.  \n",
    "_**Please do not take with you**_.\n",
    "\n",
    "# Today's menu\n",
    "\n",
    "* Clipping planes and surfaces (p 79)\n",
    "* Distances and Labels (p 82) - Wizard\n",
    "* Extract and modify ligand (p 88)\n",
    "* Display H-bonds (p 91)\n",
    "* Electrostatic potential (p 93)\n",
    "* Side chain mutation (p 98) - Wizard\n",
    "* Automatic 3D superimposition (p 102)\n",
    "* Model building (alpha helix; p 106)\n"
   ]
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   "source": [
    "## To get your own PyMOL workbook in PDF format:\n",
    "- fill-in the one page 1 page survey \"evaluation\" form for this class \n",
    "- BONUS: **Complete PDF of PyMOL workbook** used in class\n",
    "\n",
    "The evaluation is anonymous, click (or type) *either* link below:\n",
    "\n",
    "- short URL: http://go.wisc.edu/e776yf (easier to type)\n",
    "\n",
    "[If necessary survey will be unlocked when workshop occurs]\n"
   ]
  }
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