Changes examples

examples/DEER/conformation-refinement/conformer_refinement.ipynb

@@ -7,7 +7,9 @@
     "# BioEn Enemble Refinement with DEER Data\n",
     "(This Jupyter notebook documents the use of BioEn with an ensemble of conformations. For the use of BioEn spin-label reweighting, please either rotamer_refinement_potra.ipynb orrotamer_refinement.ipynb.)\n",
     "\n",
-    "By applying this ipython notebook, we can perform spin-label ensemble refinement with DEER data using BioEn. The steps of the Jupyter notebook are <br> \n",
+    "In this notebook, we perform ensemble refinement with DEER data using BioEn. Here we are interested in a small ensemble of POTRA domain structures. Note that is an illustrative example, where we optimize the weights of the ensemble members, but keep the spin-label positions as predicted by the standard spin-label rotamer library. Accounting for the spin-label positions however is crucial to properly interpret this data set as shown in Reichel et al. 2018. For some systems, the details of the spin-label positions can be neglected and this notebook can serve as a starting point to define workflows for them.  \n",
+    "\n",
+    "The steps of the Jupyter notebook are <br> \n",
     "\n",
     "1. Preparation of the input <br> \n",
     "2. BioEn <br> \n",
@@ -95,7 +97,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 1. Preparation"
+    "# 1. Preparation\n",
+    "\n",
+    "Here we are going to define a few useful functions. We will find possible spin-label positions for the different structures in our conformational ensemble. We are looking at a DEER experiment with spin labels at residues 370 and 292. \n",
+    "\n",
+    "From the spin-label positions for a given ensemble member we will calculate a DEER time trace. For each conformation in the ensemble we will obtain a DEER time trace. "
    ]
   },
   {
@@ -216,7 +222,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Get all input for BioEn"
+    "## Get all input for BioEn\n",
+    "\n",
+    "Now we are calling the functions defined above to calculate the DEER time traces for the ensemble."
    ]
   },
   {
@@ -619,7 +627,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Cummulative weight"
+    "## Analyzing weight changes.\n",
+    "\n",
+    "By looking at the cumulative weight distributions, we can get an idea of the magnitude of changes in the weights upon refining the ensemble."
    ]
   },
   {
@@ -823,31 +833,40 @@
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    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.14"
+   "version": "2.7.12"
+  },
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+   "bibliofile": "biblio.bib",
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   "toc": {
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-   "navigate_menu": true,
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-   "threshold": 4,
+   "skip_h1_title": false,
+   "title_cell": "Table of Contents",
+   "title_sidebar": "Contents",
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