Notebook tweaks

SAFEP_Tutorial_Notebook.ipynb

@@ -79,7 +79,7 @@
     "For more up-to-date and general versions see the SAFEP github.\n",
     "\n",
     "- This and other SAFEP notebooks make use of pyMBAR and Alchemlyb. \n",
-    "For more information see Shirts and Chodera (2008), \"Statistically optimal analysis of samples from multiple equilibrium states\" doi: 10.1063/1.2978177\n",
+    "For more information see Shirts and Chodera (2008), [\"Statistically optimal analysis of samples from multiple equilibrium states\"](https://doi.org/10.1063%2F1.2978177)\n",
     "\n"
    ]
   },
@@ -422,17 +422,6 @@
     "**Step E.3 to End**"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "64ae9965",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def RMS(some_vector):\n",
-    "    return np.sqrt(np.mean(np.array(some_vector)**2))"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -474,7 +463,7 @@
     "    return L/(K+L)\n",
     "\n",
     "def Kd(dG, RT):\n",
-    "    return np.exp(dG/RT)*1000"
+    "    return np.exp(dG/RT)*1000000"
    ]
   },
   {
@@ -484,14 +473,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "concentrations = np.logspace(-3,2,1000) # A vector of concentrations in millimolar\n",
+    "concentrations = np.logspace(0,5,1000) # A vector of concentrations in micromolar\n",
     "K = Kd(dG_binding, RT)\n",
     "\n",
     "fig, ax = plt.subplots(figsize=(10,6.1))\n",
     "ax.plot(concentrations, P_bind(K, concentrations), label='Binding Curve')\n",
     "ax.fill_between(concentrations, P_bind(Kd(dG_binding-error_binding*1.96, RT), concentrations), P_bind(Kd(dG_binding+error_binding*1.96, RT), concentrations), alpha=0.25, label='95% Confidence Interval')\n",
     "plt.xscale('log')\n",
-    "ax.set_xlabel('Concentration of Phenol (mM)', fontsize=20)\n",
+    "ax.set_xlabel('Concentration of Phenol '+r'($\\mathrm{\\mu}$M)', fontsize=20)\n",
     "ax.set_ylabel('Fraction of Sites Occupied', fontsize=20)\n",
     "ax.vlines(K, 0, 1, linestyles='dashed', color='black', label='Dissociation Constant')\n",
     "ax.legend(loc='lower right', fontsize=20*0.75)\n",
@@ -525,7 +514,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.12"
   }
  },
  "nbformat": 4,