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presentation.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="presentation_files/libs/clipboard/clipboard.min.js"></script>
<script src="presentation_files/libs/quarto-html/tabby.min.js"></script>
<script src="presentation_files/libs/quarto-html/popper.min.js"></script>
<script src="presentation_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="presentation_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="presentation_files/libs/quarto-html/light-border.css" rel="stylesheet">
<link href="presentation_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="presentation_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="presentation_files/libs/quarto-contrib/molstar-v3.13.0/molstar.js"></script>
<link href="presentation_files/libs/quarto-contrib/molstar-v3.13.0/molstar.css" rel="stylesheet">
<link href="presentation_files/libs/quarto-contrib/molstar-v3.13.0/app-container.css" rel="stylesheet"><meta charset="utf-8">
<meta name="generator" content="quarto-1.4.550">
<title>Molstar example</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="presentation_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="presentation_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
</style>
<link rel="stylesheet" href="presentation_files/libs/revealjs/dist/theme/quarto.css">
<link rel="stylesheet" href="presentation.css">
<link href="presentation_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="presentation_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="presentation_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="presentation_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-titled.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-titled) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-titled.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-titled .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-titled .callout-title p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-titled.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-titled.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-title {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-title {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-title {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-titled .callout-body > .callout-content > :last-child {
padding-bottom: 0.5rem;
margin-bottom: 0;
}
.callout.callout-titled .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-titled) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAAAXNSR0IArs4c6QAAAERlWElmTU0AKgAAAAgAAYdpAAQAAAABAAAAGgAAAAAAA6ABAAMAAAABAAEAAKACAAQAAAABAAAAIKADAAQAAAABAAAAIAAAAACshmLzAAAEU0lEQVRYCcVXTWhcVRQ+586kSUMMxkyaElstCto2SIhitS5Ek8xUKV2poatCcVHtUlFQk8mbaaziwpWgglJwVaquitBOfhQXFlqlzSJpFSpIYyXNjBNiTCck7x2/8/LeNDOZxDuEkgOXe++553zfefee+/OYLOXFk3+1LLrRdiO81yNqZ6K9cG0P3MeFaMIQjXssE8Z1JzLO9ls20MBZX7oG8w9GxB0goaPrW5aNMp1yOZIa7Wv6o2ykpLtmAPs/vrG14Z+6d4jpbSKuhdcSyq9wGMPXjonwmESXrriLzFGOdDBLB8Y6MNYBu0dRokSygMA/mrun8MGFN3behm6VVAwg4WR3i6FvYK1T7MHo9BK7ydH+1uurECoouk5MPRyVSBrBHMYwVobG2aOXM07sWrn5qgB60rc6mcwIDJtQrnrEr44kmy+UO9r0u9O5/YbkS9juQckLed3DyW2XV/qWBBB3ptvI8EUY3I9p/67OW+g967TNr3Sotn3IuVlfMLVnsBwH4fsnebJvyGm5GeIUA3jljERmrv49SizPYuq+z7c2H/jlGC+Ghhupn/hcapqmcudB9jwJ/3jvnvu6vu5lVzF1fXyZuZZ7U8nRmVzytvT+H3kilYvH09mLWrQdwFSsFEsxFVs5fK7A0g8gMZjbif4ACpKbjv7gNGaD8bUrlk8x+KRflttr22JEMRUbTUwwDQScyzPgedQHZT0xnx7ujw2jfVfExwYHwOsDTjLdJ2ebmeQIlJ7neo41s/DrsL3kl+W2lWvAga0tR3zueGr6GL78M3ifH0rGXrBC2aAR8uYcIA5gwV8zIE8onoh8u0Fca/ciF7j1uOzEnqcIm59sEXoGc0+z6+H45V1CvAvHcD7THztu669cnp+L0okAeIc6zjbM/24LgGM1gZk7jnRu1aQWoU9sfUOuhrmtaPIO3YY1KLLWZaEO5TKUbMY5zx8W9UJ6elpLwKXbsaZ4EFl7B4bMtDv0iRipKoDQT2sNQI9b1utXFdYisi+wzZ/ri/1m7QfDgEuvgUUEIJPq3DhX/5DWNqIXDOweC2wvIR90Oq3lDpdMIgD2r0dXvGdsEW5H6x6HLRJYU7C69VefO1x8Gde1ZFSJLfWS1jbCnhtOPxmpfv2LXOA2Xk2tvnwKKPFuZ/oRmwBwqRQDcKNeVQkYcOjtWVBuM/JuYw5b6isojIkYxyYAFn5K7ZBF10fea52y8QltAg6jnMqNHFBmGkQ1j+U43HMi2xMar1Nv0zGsf1s8nUsmUtPOOrbFIR8bHFDMB5zL13Gmr/kGlCkUzedTzzmzsaJXhYawnA3UmARpiYj5ooJZiUoxFRtK3X6pgNPv+IZVPcnwbOl6f+aBaO1CNvPW9n9LmCp01nuSaTRF2YxHqZ8DYQT6WsXT+RD6eUztwYLZ8rM+rcPxamv1VQzFUkzFXvkiVrySGQgJNvXHJAxiU3/NwiC03rSf05VBaPtu/Z7/B8Yn/w7eguloAAAAAElFTkSuQmCC');
}
div.callout-note.callout-style-default .callout-title {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
}
div.callout-important .callout-icon::before {
background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAAAXNSR0IArs4c6QAAAERlWElmTU0AKgAAAAgAAYdpAAQAAAABAAAAGgAAAAAAA6ABAAMAAAABAAEAAKACAAQAAAABAAAAIKADAAQAAAABAAAAIAAAAACshmLzAAAEKklEQVRYCcVXTWhcVRS+575MJym48A+hSRFr00ySRQhURRfd2HYjk2SSTokuBCkU2o0LoSKKraKIBTcuFCoidGFD08nkBzdREbpQ1EDNIv8qSGMFUboImMSZd4/f9zJv8ibJMC8xJQfO3HPPPef7zrvvvnvviIkpC9nsw0UttFunbUhpFzFtarSd6WJkStVMw5xyVqYTvkwfzuf/5FgtkVoB0729j1rjXwThS7Vio+Mo6DNnvLfahoZ+i/o32lULuJ3NNiz7q6+pyAUkJaFF6JwaM2lUJlV0MlnQn5aTRbEu0SEqHUa0A4AdiGuB1kFXRfVyg5d87+Dg4DL6m2TLAub60ilj7A1Ec4odSAc8X95sHh7+ZRPCFo6Fnp7HfU/fBng/hi10CjCnWnJjsxvDNxWw0NfV6Rv5GgP3I3jGWXumdTD/3cbEOP2ZbOZp69yniG3FQ9z1jD7bnBu9Fc2tKGC2q+uAJOQHBDRiZX1x36o7fWBs7J9ownbtO+n0/qWkvW7UPIfc37WgT6ZGR++EOJyeQDSb9UB+DZ1G6DdLDzyS+b/kBCYGsYgJbSQHuThGKRcw5xdeQf8YdNHsc6ePXrlSYMBuSIAFTGAtQo+VuALo4BX83N190NWZWbynBjhOHsmNfFWLeL6v+ynsA58zDvvAC8j5PkbOcXCMg2PZFk3q8MjI7WAG/Dp9AwP7jdGBOOQkAvlFUB+irtm16I1Zw9YBcpGTGXYmk3kQIC/Cds55l+iMI3jqhjAuaoe+am2Jw5GT3Nbz3CkE12NavmzN5+erJW7046n/CH1RO/RVa8lBLozXk9uqykkGAyRXLWlLv5jyp4RFsG5vGVzpDLnIjTWgnRy2Rr+tDKvRc7Y8AyZq10jj8DqXdnIRNtFZb+t/ZRtXcDiVnzpqx8mPcDWxgARUqx0W1QB9MeUZiNrV4qP+Ehc+BpNgATsTX8ozYKL2NtFYAHc84fG7ndxUPr+AR/iQSns7uSUufAymwDOb2+NjK27lEFocm/EE2WpyIy/Hi66MWuMKJn8RvxIcj87IM5Vh9663ziW36kR0HNenXuxmfaD8JC7tfKbrhFr7LiZCrMjrzTeGx+PmkosrkNzW94ObzwocJ7A1HokLolY+AvkTiD/q1H0cN48c5EL8Crkttsa/AXQVDmutfyku0E7jShx49XqV3MFK8IryDhYVbj7Sj2P2eBxwcXoe8T8idsKKPRcnZw1b+slFTubwUwhktrfnAt7J++jwQtLZcm3sr9LQrjRzz6cfMv9aLvgmnAGvpoaGLxM4mAEaLV7iAzQ3oU0IvD5x9ix3yF2RAAuYAOO2f7PEFWCXZ4C9Pb2UsgDeVnFSpbFK7/IWu7TPTvBqzbGdCHOJQSxiEjt6IyZmxQyEJHv6xyQsYk//moVFsN2zP6fRImjfq7/n/wFDguUQFNEwugAAAABJRU5ErkJggg==');
}
div.callout-important.callout-style-default .callout-title {
background-color: #f7dddc
}
div.callout-warning {
border-left-color: #f0ad4e !important;
}
div.callout-warning .callout-icon::before {
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<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Molstar example</h1>
<div class="quarto-title-authors">
</div>
</section>
<section id="rcsb-pdb" class="slide level2">
<h2>RCSB PDB</h2>
<p>Get a protein from the RCSB PDB with:</p>
<p><code>{{< mol-rcsb 7sgl >}}</code></p>
<iframe id="app-7sgl" class="molstar-app" seamless="" allow="fullscreen" srcdoc="
<html>
<head>
<script type="text/javascript" src="./molstar.js"></script>
<link rel="stylesheet" type="text/css" href="./molstar.css"/>
</head>
<body>
<div id="app-7sgl" class="molstar-app"></div>
<script type="text/javascript">
molstar.Viewer.create("app-7sgl", {"layoutShowLog":false,"layoutIsExpanded":false,"layoutShowControls":false,"emdbProvider":"rcsb","pdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowRemoteState":false,"viewportShowExpand":true,"layoutShowLeftPanel":true,"layoutShowSequence":false,"viewportShowSelectionMode":false}).then(viewer => {
viewer.loadPdb("7sgl"); });
</script>
</body>
</html>
">
</iframe>
</section>
<section id="local-pdb-file" class="slide level2">
<h2>Local pdb file</h2>
<p>Get a local pdb file with:</p>
<p><code>{{< mol-url ./www/7sgl.pdb >}}</code></p>
<iframe id="app-./www/7sgl.pdb" class="molstar-app" seamless="" allow="fullscreen" srcdoc="
<html>
<head>
<script type="text/javascript" src="./molstar.js"></script>
<link rel="stylesheet" type="text/css" href="./molstar.css"/>
</head>
<body>
<div id="app-./www/7sgl.pdb" class="molstar-app"></div>
<script type="text/javascript">
molstar.Viewer.create("app-./www/7sgl.pdb", {"layoutShowLog":false,"layoutIsExpanded":false,"layoutShowControls":false,"emdbProvider":"rcsb","pdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowRemoteState":false,"viewportShowExpand":true,"layoutShowLeftPanel":true,"layoutShowSequence":false,"viewportShowSelectionMode":false}).then(viewer => {
viewer.loadStructureFromUrl("./www/7sgl.pdb", format="pdb"); });
</script>
</body>
</html>
">
</iframe>
</section>
<section id="pdb-file-from-url" class="slide level2">
<h2>pdb file from url</h2>
<p>Get a pdb file from a url:</p>
<p><code>{{< mol-url https://files.rcsb.org/download/7sgl.pdb >}}</code></p>
<iframe id="app-https://files.rcsb.org/download/7sgl.pdb" class="molstar-app" seamless="" allow="fullscreen" srcdoc="
<html>
<head>
<script type="text/javascript" src="./molstar.js"></script>
<link rel="stylesheet" type="text/css" href="./molstar.css"/>
</head>
<body>
<div id="app-https://files.rcsb.org/download/7sgl.pdb" class="molstar-app"></div>
<script type="text/javascript">
molstar.Viewer.create("app-https://files.rcsb.org/download/7sgl.pdb", {"layoutShowLog":false,"layoutIsExpanded":false,"layoutShowControls":false,"emdbProvider":"rcsb","pdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowRemoteState":false,"viewportShowExpand":true,"layoutShowLeftPanel":true,"layoutShowSequence":false,"viewportShowSelectionMode":false}).then(viewer => {
viewer.loadStructureFromUrl("https://files.rcsb.org/download/7sgl.pdb", format="pdb"); });
</script>
</body>
</html>
">
</iframe>
</section>
<section id="local-xyz-file" class="slide level2">
<h2>local xyz file</h2>
<p>Get a local xyz file with:</p>
<p><code>[]{.quarto-shortcode__-escaped data-is-shortcode="1" data-value=" }</code></p>
<p>{{< mol-url ./www/example.xyz >}}</p>
</section>
<section id="local-pdb-and-trajectory" class="slide level2">
<h2>local pdb and trajectory</h2>
<p>Load a topology and a trajectory with:</p>
<p><code>{{{< mol-traj ./www/example.pdb ./www/example.xtc >}}"}</code></p>
<iframe id="app-./www/example.pdb./www/example.xtc" class="molstar-app" seamless="" allow="fullscreen" srcdoc="
<html>
<head>
<script type="text/javascript" src="./molstar.js"></script>
<link rel="stylesheet" type="text/css" href="./molstar.css"/>
</head>
<body>
<div id="app-./www/example.pdb./www/example.xtc" class="molstar-app"></div>
<script type="text/javascript">
molstar.Viewer.create("app-./www/example.pdb./www/example.xtc", {"layoutShowLog":false,"layoutIsExpanded":false,"layoutShowControls":false,"emdbProvider":"rcsb","pdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowRemoteState":false,"viewportShowExpand":true,"layoutShowLeftPanel":true,"layoutShowSequence":false,"viewportShowSelectionMode":false}).then(viewer => {
viewer.loadTrajectory(
{
model: {
kind: "model-url", url: "./www/example.pdb", format: "pdb"
},
coordinates: {
kind: "coordinates-url", url: "./www/example.xtc",
format: "xtc", isBinary: true
}
}
);
});
</script>
</body>
</html>
">
</iframe>
</section>
<section id="local-pdb-with-higher-resolution" class="slide level2">
<h2>local pdb with higher resolution</h2>
<p><code>{{< mol-url ./www/7sgl.pdb pixelScale=3 >}}</code></p>
<iframe id="app-./www/7sgl.pdb" class="molstar-app" seamless="" allow="fullscreen" srcdoc="
<html>
<head>
<script type="text/javascript" src="./molstar.js"></script>
<link rel="stylesheet" type="text/css" href="./molstar.css"/>
</head>
<body>
<div id="app-./www/7sgl.pdb" class="molstar-app"></div>
<script type="text/javascript">
molstar.Viewer.create("app-./www/7sgl.pdb", {"layoutShowLog":false,"layoutIsExpanded":false,"layoutShowControls":false,"pixelScale":"3","emdbProvider":"rcsb","pdbProvider":"rcsb","viewportShowAnimation":true,"layoutShowRemoteState":false,"viewportShowExpand":true,"layoutShowLeftPanel":true,"layoutShowSequence":false,"viewportShowSelectionMode":false}).then(viewer => {
viewer.loadStructureFromUrl("./www/7sgl.pdb", format="pdb"); });
</script>
</body>
</html>
">
</iframe>
<div class="quarto-auto-generated-content">
<div class="footer footer-default">
</div>
</div>
</section>
</div>
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