minor

Author: marscher

notebooks/00-pentapeptide-showcase.ipynb

@@ -233,7 +233,7 @@
     "\n",
     "The goal of the next step is to find a function that maps the usually high-dimensional input space into some lower-dimensional space that captures the important dynamics. The recommended way of doing so is a time-lagged independent component analysis (TICA), <a id=\"ref-4\" href=\"#cite-tica2\">molgedey-94</a>, <a id=\"ref-5\" href=\"#cite-tica\">perez-hernandez-13</a>. We perform TICA (with kinetic map scaling) using the lag time obtained from the VAMP-2 score.\n",
     "\n",
-    "By using the tica() function's default parameters, we will use as many dimensions in order to preserve $95\\%$ of the kinetic variance. By default, tica() also applies a kinetic map scaling.\n",
+    "By using the tica() function's default parameters, we will use as many dimensions as necessary in order to preserve $95\\%$ of the kinetic variance. By default, tica() also applies a kinetic map scaling.\n",
     "This scaling ensures that Euclidean distances in the projected space approximate kinetic distances,\n",
     "which is beneficial during the subsequent discretization.\n",
     "\n",

notebooks/01-data-io-and-featurization.ipynb

@@ -377,8 +377,7 @@
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-    "As we see, the score for the heavy atom positions is much higher as the one for the $\\phi/\\psi$ torsion angles. The feature with a higher score should be favored for further analysis, because it means that this feature contains more information about slow processes. If you are already digging deeper into your system of interest, you can of course restrict the analysis to features you know they are covering your process of interest no matter of its VAMP score.\n",
-    "\n",
+    "As we see, the score for the heavy atom positions is much higher as the one for the $\\phi/\\psi$ torsion angles. The feature with a higher score should be favored for further analysis, because it means that this feature contains more information about slow processes. If you are already digging deeper into your system of interest, you can of course restrict the analysis to a set of features you already know describes your process of interest, regardless of its VAMP score.\n",
     "\n",
     "Another featurization that is interesting especially for proteins is heavy atom distances:"
    ]
@@ -934,12 +933,7 @@
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