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thickcurv.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>Membrane Thickness & Curvature</title>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<style>
#gui { position: absolute; top: 55.4em; right: 30em }
</style>
<link href="https://fonts.googleapis.com/css?family=Poppins:100,200,400,300,500,600,700" rel="stylesheet">
<link rel="stylesheet" href="css/linearicons.css">
<link rel="stylesheet" href="css/bootstrap.css">
<link rel="stylesheet" href="css/main_2.css">
<link rel="stylesheet" href="css/pace.css">
<script src="js/jquery-2.2.4.min.js"></script>
<script src="js/jquery.nice-select.min.js"></script>
<script src="js/jquery.sticky.js"></script>
<script src="js/main.js"></script>
<script src="js/pace.min.js"></script>
</head>
<body>
<!-- Start Header Area -->
<header class="default-header">
<div class="container">
<div class="header-wrap">
<div class="header-top d-flex justify-content-between align-items-center">
<div class="logo">
<a href="index.html"><img src="img/logo.png" height="37" width="124"></a>
</div>
<div class="main-menubar d-flex align-items-center">
<nav class="hide">
<a href="index.html">Home</a>
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<a href="references.html">References</a>
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</nav>
<div class="menu-bar"><span class="lnr lnr-menu"></span></div>
</div>
</div>
</div>
</div>
</header>
<div>
<h1 style="font-size: 60px; text-align: center; padding-top: 70px">THICKNESS & CURVATURE</h1>
</div>
<div style="text-align: center; padding-top: 30px">
<p id="article-space" style="max-width: 60em; padding-top: 15px ; text-align: justify; margin: auto; color: red;">
This application has not been optimized for Microsoft Edge and thus may not work. Please switch to a different
browser, preferably Google Chrome.
</p>
<p id="article-space" style="max-width: 60em; padding-top: 15px ; text-align: justify; margin: auto;">
Analysis of membrane deformations as a result of embedded proteins in terms of lipid-protein interactions usually come secondary to
the analysis of individual interactions of proteins with lipids, and they are even less frequently visualized in detail. The importance
of the bulk lipid environment has been noted in the literature, in particular for GPCRs.
<br><br>
Using this application, we can visualize membrane thickness and curvature in great detail. The calculation method for the thickness and
curvature profiles uses g_surf, a tool developed by our group and described
<a href="https://pubs.acs.org/doi/full/10.1021/acscentsci.8b00143" target="_blank">here</a>. As described in the paper
g_surf uses three interpolated grid-surfaces (upper, middle, and lower) from which thickness and curvature are calculated.
Surface averages are calculated for the last 5 μs of simulation trajectories.
<br><br>
The application visualizes these results in an interactive format. You can visualize the results as either a point or surface mesh presentation.
Each has its own options and parameters which can be tweaked to allow the user to select a part of the figure and control the detail of whatever aspect
of it. We also show the position of embedded proteins as a point presentation with a coloring scheme that runs from black to red to pink to white as
the GPCR sequence goes from TM1 to TM7/8. This makes it possible to clearly see which part of the protein is causing what deformation in the membrane.
Considering that there are four protein copies in our simulation setups, this also allows for the comparison of the deformation caused by one protein
to the others, as considering the size of the systems, each proteins' activity should be independent to that of the others'.
</p>
<p id="article-space" style="max-width: 60em; padding-top: 30px ; text-align: justify; margin: auto;"></p>
<div id="thickcurve" class="thickcurve" style="max-width: 80em; height: 45em; text-align: justify; margin: auto;"></div>
<script src="js/threejs/three.min.js"></script>
<script src="js/threejs/PLYLoader.js"></script>
<script src="js/threejs/TrackballControls.js"></script>
<script src="js/threejs/WebGL.js"></script>
<script src="js/threejs/Lut.js"></script>
<script src="js/threejs/dat.gui.min.js"></script>
<script src="js/threejs/thickcurve.js"></script>
<script>
guis = {}
function createElement(name, properties, style) {
var el = document.createElement(name)
Object.assign(el, properties)
Object.assign(el.style, style)
return el
}
function createSelect(options, properties, style) {
var select = createElement("select", properties, style)
options.forEach(function (d) {
select.add(createElement("option", {
value: d[0],
text: d[1]
}))
})
return select
}
var exampleSelect = createSelect([
["5HT1B", "5HT1B"],
["A2ARa", "A2ARa"],
["A2ARi", "A2ARi"],
["ApelinR", "ApelinR"],
["AT2R", "AT2R"],
["b2ARa", "b2ARa"],
["b2ARi", "b2ARi"],
["CalcitoninR", "CalcitoninR"],
["CB1R", "CB1R"],
["D3R", "D3R"],
["ETbR", "ETbR"],
["GLP1", "GLP1"],
["GlucagonR", "GlucagonR"],
["H1R", "H1R"],
["LPAR1", "LPAR1"],
["M2Ra", "M2Ra"],
["M2Ri", "M2Ri"],
["mGlu5", "mGlu5"],
["mORa", "mORa"],
["mORi", "mORi"],
["OX2R", "OX2R"],
["PAR2", "PAR2"],
["RhodRa", "RhodRa"],
["RhodRi", "RhodRi"],
["S1PR1", "S1PR1"],
["SMO", "SMO"],
["US28", "US28"],
], {
onchange: function (e) {
var id = e.target.value;
document.getElementById("thickcurve").innerHTML = "";
document.getElementById("thickcurve").appendChild(exampleSelect)
scene = thickcurve(id)
gui = guis['g'];
gui.destroy();
}
}, {
top: "0em",
left: "0em"
})
exampleSelect.setAttribute("id", "soflow-color");
document.getElementById("thickcurve").appendChild(exampleSelect)
document.getElementsByTagName("select")[0].value = "5HT1B"
scene = thickcurve("5HT1B");
</script>
<div style="text-align: center; padding-top: 60px">
<p id="article-space" style="max-width: 60em; padding-top: 75px ; text-align: justify; margin: auto;">
A few more things to note:
<br><br>
- The application uses <a href="https://threejs.org/"" target="_blank">Three.js</a> to display the data within the browser, but the mean and gaussian
curvature colorschemes are calculated using <a href="http://www.meshlab.net/" target="_blank">Meshlab</a>.
<br><br>
- Please note that the Gaussian curvature calculated by MeshLab differs slightly from the same calculation done by g_surf.
<br><br>
- You can toggle the visibility of each layer of the plot.
<br><br>
</p>
<p id="article-space" style="max-width: 60em; padding-top: 30px ; text-align: justify; margin: auto;"></p>
</div>
</body>
</html>