fixed image + added code tags to PyMOL commands

Author: LoganColeNIH

images/4I8N.png

@@ -43,8 +43,8 @@
    "id": "acd1fbfe-9b1c-44a5-af58-1ab689e68d10",
    "metadata": {},
    "source": [
-    "PyMOL> pwd  \n",
-    "PyMOL> ls \n"
+    "<code>PyMOL> pwd </code><br>\n",
+    "<code>PyMOL> ls </code>\n"
    ]
   },
   {
@@ -108,7 +108,7 @@
    "id": "51f4bb95-4003-4534-83b4-d697c17adbe0",
    "metadata": {},
    "source": [
-    "PyMOL> fetch 1AKI."
+    "<code>PyMOL> fetch 1AKI</code>"
    ]
   },
   {
@@ -130,8 +130,8 @@
    "id": "6ec55c64-17a7-439f-87cf-704a92e00712",
    "metadata": {},
    "source": [
-    "PyMOL> ray 1000,1000 <br>\n",
-    "PyMOL> png lysozyme.png"
+    "<code><PyMOL> ray 1000,1000</code> <br>\n",
+    "<code>PyMOL> png lysozyme.png<code>"
    ]
   },
   {
@@ -277,7 +277,7 @@
     "\n",
     "Create a new PyMOL window (or delete everything in your current session). In the PyMOL command line, type\n",
     "\n",
-    "PyMOL> fetch 4I8N"
+    "<code>PyMOL> fetch 4I8N</code>"
    ]
   },
   {
@@ -286,16 +286,18 @@
    "id": "23bbcd64-7b83-40ba-8c1b-56f1a27a8a1d",
    "metadata": {},
    "source": [
-    "![GTQBioS-Tutorial1-May15-4.jpg](attachment:9bb5711d-4517-4fcc-a056-fffe7f6e8df4.jpg)\n",
-    "Figure 4: PTP1B protein (PDBID: 4I8N).\n",
+    "<p align=\"center\">\n",
+    "    <img src=\"images/4I8N.png\" width=\"800\" />\n",
+    "</p>\n",
+    "Figure 4: PTP1B protein (PDBID: 4I8N).<br><br>\n",
     "\n",
     "Color by secondary structure and observe your protein, which should look like Figure 4 (note: the colors used here are different from the default; feel free to explore different color palettes for your protein structure). This protein is called protein tyrosine phosphatase 1B (PTP1B), and functions to remove phosphate groups from molecules. For the sake of this tutorial, it is important only to know that this protein can be inhibited,\n",
     "and that an inhibitor molecule is also found within this pdb file. Typically, when loading in a pdb file containing both a protein and a ligand, the protein will be automatically visualized in ‘cartoon’ format and\n",
     "the ligand in ‘licorice’ format. This makes it easy to identify the ligand upon first loading of the molecule. PTP1B is an interesting protein because we can directly compare it to other proteins within the same PTP\n",
     "family. For instance, type into the command line\n",
     "\n",
-    "PyMOL> fetch 1L8K<br>\n",
-    "PyMOL> align 4I8N, 1L8K"
+    "<code>PyMOL> fetch 1L8K</code><br>\n",
+    "<code>PyMOL> align 4I8N, 1L8K</code>"
    ]
   },
   {
@@ -455,9 +457,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel) (Local) (Local)",
+   "display_name": "conda_python3",
    "language": "python",
-   "name": "conda-base-py"
+   "name": "conda_python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -469,7 +471,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.16"
+   "version": "3.10.18"
   }
  },
  "nbformat": 4,