Rename notebook files

Author: CharlieLaughton

.PCA_analysis_of_MD_simulations-1.ipynb PCA_analysis_of_MD_simulations-1.ipynb.PCA_analysis_of_MD_simulations-1.ipynb renamed to PCA_analysis_of_MD_simulations-1.ipynb

@@ -254,7 +254,7 @@
     "\n",
     "#### Compare the RMSD and PCA plots. Consider how clearly they identify the similarities and differences between the two trajectories, and illustrate sampling and convergence.\n",
     "\n",
-    "[Next: Part 2: Analysis of replicate simulations of dynein light chain](.PCA_analysis_of_MD_simulations-2.ipynb)"
+    "[Next: Part 2: Analysis of replicate simulations of dynein light chain](PCA_analysis_of_MD_simulations-2.ipynb)"
    ]
   },
   {
@@ -267,7 +267,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -281,9 +281,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }

.PCA_analysis_of_MD_simulations-2.ipynb PCA_analysis_of_MD_simulations-2.ipynb.PCA_analysis_of_MD_simulations-2.ipynb renamed to PCA_analysis_of_MD_simulations-2.ipynb

@@ -160,7 +160,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -174,9 +174,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }

PCA_analysis_of_MD_simulations.ipynb

@@ -93,16 +93,26 @@
    "cell_type": "markdown",
    "metadata": {
     "collapsed": true,
-    "hidden": true
+    "hidden": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
-    "[Next: Part 1: Comparison of trajectories of wild-type neuraminidase and of the I233R/H275Y (IRHY) double mutant.](.PCA_analysis_of_MD_simulations-1.ipynb)"
+    "[Next: Part 1: Comparison of trajectories of wild-type neuraminidase and of the I233R/H275Y (IRHY) double mutant.](PCA_analysis_of_MD_simulations-1.ipynb)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -116,9 +126,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }