fixes

Author: IAlibay

cookbook/openfold3_to_openfe.ipynb

@@ -51,9 +51,10 @@
     "\n",
     "2. Processing the OpenFold3 output for use with OpenFE\n",
     "\n",
-    "  - Choosing a reference protein structure\n",
-    "  - Aligning & extracting the ncessary ligands & protein structures.\n",
-    "  - Fixing & protonating the reference protein structure.\n",
+    "  * a) Choosing a reference protein structure\n",
+    "  * b) Aligning & extracting the ncessary ligands & protein structures.\n",
+    "  * c) Fixing & protonating the reference protein structure.\n",
+    "\n",
     "\n",
     "3. Loading structures into OpenFE Components\n",
     "\n",
@@ -226,19 +227,19 @@
     "Now that we have a set of predicted structures, we must extract the relevant information from the PDB files.\n",
     "This means:\n",
     "\n",
-    "1. Choosing a reference protein structure which will be used for all binding affinity predictions\n",
+    "a) Choosing a reference protein structure which will be used for all binding affinity predictions\n",
     "\n",
     "  - This is necessary for RBFE simulations, where a single structure must be kept constant throughout the transformations. Note that for ABFE simulations, this step can be avoided.\n",
     "  - For the sake of this demonstration, we will be choosing the predicted structure that is bound to the ligand occupying the largest volume. The idea here being that hopefully the binding site of that structure can accomodate all the other ligands. We note that in practice this is not always true.\n",
     "\n",
-    "2. Aligning the structures to the reference & extracting the necessary structures\n",
+    "b) Aligning the structures to the reference & extracting the necessary structures\n",
     "\n",
-    "  - This is so that we can extract the ligands and use them with the chosen structure.\n",.\n",
+    "  - This is so that we can extract the ligands and use them with the chosen structure.\n",
     "\n",
-    "3. Fixing & protonating the reference protein structure.\n",
+    "c) Fixing & protonating the reference protein structure.\n",
     "\n",
     "\n",
-    "#### Choosing a reference protein structure\n",
+    "#### a) Choosing a reference protein structure\n",
     "\n",
     "As mentioned above, we will select a reference protein structure for all simulations going forward. To do this, we naively select the structure bound to a ligand with the largest volume.\n",
     "\n",
@@ -366,7 +367,7 @@
    "id": "6056e755-0da0-4712-b4ae-7a721c94851d",
    "metadata": {},
    "source": [
-    "#### Aligning & extracting the necessary structures\n",
+    "#### b) Aligning & extracting the necessary structures\n",
     "\n",
     "Next we align all the models back to the reference structure. We then extract all the ligands and the protein atoms from the reference."
    ]
@@ -476,7 +477,7 @@
    "id": "10b42b56-2f47-4215-8397-fcf7473c4860",
    "metadata": {},
    "source": [
-    "#### Fixing & protonating the reference protein structure\n",
+    "#### c) Fixing & protonating the reference protein structure\n",
     "\n",
     "The PDB contains the heavy atoms of the protein but is missing hydrogens and caps. Here we call PDBFixer to add hydrogens at pH 7 and add protein caps."
    ]
@@ -498,7 +499,7 @@
    ],
    "source": [
     "# now run the reference protein through pdbfixer\n",
-    "%% bash\n"
+    "%% bash\n",
     "pdbfixer assets/of3_output/p_aligned/protein.pdb --add-atoms=all --add-residues --output=assets/of3_output/p_aligned/protein_fixed.pdb"
    ]
   },