{ "cells": [ { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Conformational analysis of CXCL12" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "-" } }, "source": [ "In this tutorial, we demonstrate how to use the HTMD code for doing conformational analysis.\n", "\n", "To analyze, one needs MD trajectories first, which can be generated with HTMD. Here, we already provide the trajectories (data) to analyze. You can download the data from [here](http://pub.htmd.org/tutorials/cxcl12-conformational-analysis/filtered.tar.gz). (**Warning: 2.6 GB filesize**)\n", "\n", "Alternatively, you can download the dataset using `wget`." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "import os\n", "assert os.system('wget -rcN -np -nH -q --cut-dirs=2 -R index.html* http://pub.htmd.org/tutorials/cxcl12-conformational-analysis/filtered/') == 0" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## Getting started" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "First we import the modules we are going to need for the tutorial:" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "slideshow": { "slide_type": "-" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Populating the interactive namespace from numpy and matplotlib\n", "\n", "Please cite HTMD: Doerr et al.(2016)JCTC,12,1845. \n", "https://dx.doi.org/10.1021/acs.jctc.6b00049\n", "Documentation: http://software.acellera.com/\n", "To update: conda update htmd -c acellera -c psi4\n", "\n", "You are on the latest HTMD version (unpackaged : /home/joao/maindisk/software/repos/Acellera/htmd/htmd).\n", "\n" ] } ], "source": [ "%pylab inline\n", "from htmd.ui import *\n", "config(viewer='webgl')" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "## Introduction to CXCL12" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "-" } }, "source": [ "CXCL12 is a chemokine involved in...\n", "\n", "* many types of cancer \n", "* inflammatory diseases \n", "* early development events" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "-" } }, "source": [ "
\n", " | atomIndexes | \n", "description | \n", "type | \n", "
---|---|---|---|
22 | \n", "[253, 255, 262, 264] | \n", "Sine of angle of (SER 16 N A A) (SER 16 CA A A... | \n", "dihedral | \n", "
23 | \n", "[253, 255, 262, 264] | \n", "Cosine of angle of (SER 16 N A A) (SER 16 CA A... | \n", "dihedral | \n", "
28 | \n", "[262, 264, 266, 279] | \n", "Sine of angle of (SER 16 C A A) (HSD 17 N A A)... | \n", "dihedral | \n", "
55 | \n", "[371, 373, 391, 393] | \n", "Cosine of angle of (LYS 24 N A A) (LYS 24 CA A... | \n", "dihedral | \n", "
140 | \n", "[723, 725, 727, 737] | \n", "Sine of angle of (ASN 44 C A A) (ASN 45 N A A)... | \n", "dihedral | \n", "