Updates based on feedback from...

* Sander Roet
* Peter Bolhuis
* UvA BioMolSim 2020

Author: dwhswenson

1_tps_sampling_tutorial.ipynb

@@ -164,7 +164,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "There's only one pair of Ramachandran angles of interest here: the ones for residue 1, alanine. To figure out which atoms are needed, we use the definition of $\\phi_i$, which tells us we need C$^{(0)}$, N$^{(1)}$, C$_\\alpha^{(1)}$, and C$^{(1)}$; i.e., `ACE0-C`, `ALA1-N`, `ALA1-CA`, and `ALA1-C`. We can find the correct atom indices from the result of the previous cell. "
+    "There's only one pair of Ramachandran angles of interest here: the ones for residue 1, alanine. To figure out which atoms are needed, we use the definition of $\\phi_i$, which tells us we need C$^{(0)}$, N$^{(1)}$, C$_\\alpha^{(1)}$, and C$^{(1)}$; i.e., `ACE1-C`, `ALA2-N`, `ALA2-CA`, and `ALA2-C`. We can find the correct atom indices from the result of the previous cell. "
    ]
   },
   {
@@ -173,7 +173,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# ACE0-C, ALA1-N, ALA1-CA, ALA1-C: 4,6,8,14\n",
+    "# ACE1-C, ALA2-N, ALA2-CA, ALA2-C: 4,6,8,14\n",
     "phi = paths.MDTrajFunctionCV(\"phi\", md.compute_dihedrals, engine.topology, indices=[[4,6,8,14]])"
    ]
   },

2_tps_analysis_tutorial.ipynb

@@ -130,6 +130,7 @@
    "source": [
     "md_traj = traj.to_mdtraj().image_molecules()\n",
     "view = nv.show_mdtraj(md_traj)\n",
+    "view.clear()\n",
     "view.add_ball_and_stick(\"ACE ALA NME\")\n",
     "view.center()\n",
     "view"
@@ -139,7 +140,10 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Double-clicking the viewing window makes it go full screen. You can also pan, zoom, and rotate using the mouse.\n",
+    "Click the two arrows in the upper right to go full screen. You can also pan, zoom, and rotate using the mouse.\n",
+    "\n",
+    "If you do not see the widget, you may still need to run the command to enable the widget (and to restart Jupyter):\n",
+    "`jupyter-nbextension enable nglview --py --sys-prefix`\n",
     "\n",
     "Note that you can also save the trajectory in a format that VMD can read, and then you could use VMD instead.\n",
     "\n",
@@ -434,34 +438,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "If you have the full simulation data, you can visualize these trajectories with NGLView. (Full simulation data not provided online, due to size)."
+    "If you have the full simulation data, you could visualize these trajectories with NGLView. (Full simulation data not provided online, due to size), using the same approach as above."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "#md_trajA = trajA.to_mdtraj().image_molecules()\n",
-    "#view_A = nv.show_mdtraj(md_trajA)\n",
-    "#view_A.add_ball_and_stick(\"ACE ALA NME\")\n",
-    "#view_A.center()\n",
-    "#view_A"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#md_trajB = trajB.to_mdtraj().image_molecules()\n",
-    "#view_B = nv.show_mdtraj(md_trajB)\n",
-    "#view_B.add_ball_and_stick(\"ACE ALA NME\")\n",
-    "#view_B.center()\n",
-    "#view_B"
-   ]
+   "source": []
   }
  ],
  "metadata": {

3_committor_analysis_tutorial.ipynb

@@ -236,7 +236,7 @@
    "source": [
     "You'll notice that this is *not* very sharply peaked in $\\psi$. This means that $\\psi$ alone probably doesn't define the transition state.\n",
     "\n",
-    "If $\\psi$ did define the transition state, we'd probably expect the transition state to be around $\\psi = 0.6$ (~35 degrees) to $\\psi = 1.0$ (~60 degrees). Now, instead of keeping the committor probability fixed and histogramming the values of $\\psi$, let's see what the values of the committor are for a fixed value of $\\psi = \\psi^*$. If $\\psi^*$ defined the transition state, then the committor would always be 0.5 here."
+    "If $\\psi$ did define the transition state, we'd probably expect the transition state to be around $\\psi = 0.6$ (\\~35 degrees) to $\\psi = 1.0$ (\\~60 degrees). Now, instead of keeping the committor probability fixed and histogramming the values of $\\psi$, let's see what the values of the committor are for a fixed value of $\\psi = \\psi^*$. If $\\psi^*$ defined the transition state, then the committor would always be 0.5 here."
    ]
   },
   {
@@ -297,6 +297,7 @@
     "# YOUR TURN: modify the snapshot number; compare the conformations\n",
     "md_traj_A = paths.Trajectory([isocommittor_0x5[2]]).to_mdtraj().image_molecules()\n",
     "view_A = nv.show_mdtraj(md_traj_A)\n",
+    "view_A.clear()\n",
     "view_A.add_ball_and_stick(\"ACE ALA NME\")\n",
     "view_A.center()\n",
     "view_A"

5_advanced_customize_shooting.ipynb

@@ -386,7 +386,7 @@
    "source": [
     "## Comparing two-way shooting to biased shooting\n",
     "\n",
-    "Let's open the "
+    "Let's open the output file and analyze the results."
    ]
   },
   {
@@ -542,7 +542,8 @@
    "outputs": [],
    "source": [
     "ens_0_strategy = strategies.OneWayShootingStrategy(\n",
-    "    ensembles=[tis_network.sampling_ensembles[0]]\n",
+    "    ensembles=[tis_network.sampling_ensembles[0]],\n",
+    "    engine=engine\n",
     ")"
    ]
   },