{ "cells": [ { "cell_type": "markdown", "metadata": { "tags": [] }, "source": [ "# Missing Contacts\n", "You might find that some contacts that you were **expecting** to be found by ``mdciao`` don't actually show up in ``mdciao``'s results. Several input parameters control the contact reporting of ``mdciao``, and it might not be obvious which one of them (if any) is actually *hiding* your contact. The logic behind these parameters, and their default values, is fairly straightforward, and we illustrate it here.\n", "\n", "\n", "If you want to run this notebook on your own, please download and extract the data from [here](http://proteinformatics.org/mdciao/mdciao_example.zip) first. You can download it:\n", "\n", "* using the browser \n", "* using the terminal with \n", " ```wget http://proteinformatics.org/mdciao/mdciao_example.zip; unzip mdciao_example.zip```\n", "* using mdciao's own method [mdciao.examples.fetch_example_data](http://proteinformatics.uni-leipzig.de/mdciao/api/generated/generated/mdciao.examples.fetch_example_data.html?highlight=fetch)\n", "\n", "If you want to take a 3D-look at this data, you can do it [here](http://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/mdciao/gs-b2ar.ngl)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## `ctc_cutoff_Ang`\n", "This is the most obvious parameter that controls the contact computation. It appears virtually in all methods (CLI or API) that compute contact frequencies. Whenever it has a default value, it is **4.5 Angstrom**.\n", "\n", "