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<html>
<head>
<link rel="icon" href="../../chimera/chimera16.png" type="image/png">
<link rel="stylesheet" href="../../css/cgl.css" type="text/css">
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<title>CDDApp: Integrating Conserved Domains Database web interface with Cytoscape</title>
</head>
<body alink="#7f1066" bgcolor="#ffffff" link="#154c5c" vlink="#7f1066">
<a name="top"></a>
<!-- Top menu -->
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</div>
<!-- Left hand quick-links -->
<div class="leftNav">
<p class="header" style="margin-top: 0px">Current Plugins</p>
<h4 class="menu">Structure Integration</h4>
<h5 class="menu"><a href="../structureViz/index.html">structureViz</a></h5>
<h4 class="menu">Chem Informatics</h4>
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<h5 class="menu"><a href="../groups/index.html#groupTool">Group Tool</a></h5>
<h5 class="menu"><a href="../groups/index.html#namedSelection">Named Selection Plugin</a></h5>
<h5 class="menu"><a href="../groups/index.html#metaNodePlugin">MetaNode Plugin</a></h5>
<h4 class="menu"><a href="../utilities/index.html">Utilities</a></h4>
<h5 class="menu"><a href="../utilities/index.html#addParentNeighbors">Add Parent Neighbors</a></h5>
<h5 class="menu"><a href="../utilities/index.html#commandTool">Command tool</a></h5>
<h5 class="menu"><a href="../utilities/index.html#edgeLength">Edge Length Plugin</a></h5>
<h5 class="menu"><a href="../utilities/index.html#edgeLister">Edge Lister Plugin</a></h5>
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<h5 class="menu"><a href="../samples/index.html#tunableSampler">Tunables Sampler</a></h5>
</div>
<div class="leftInfo" style="font-size: 90%">
<p class="header" style="margin-top: 0px">Typographic Conventions</p>
<b class="mouse">Mouse button</b><br style="margin-bottom: 5px"/>
<b class="button">Dialog button</b><br style="margin-bottom: 5px"/>
<b class="button">Keyboard button</b><br style="margin-bottom: 5px"/>
<b class="menuItem">Menu item</b><br style="margin-bottom: 5px"/>
<b class="menuLabel">Dialog label</b>
</div>
<p>
<i>CDDApp</i> is a <a href="http://www.cytoscape.org" target="_blank">
Cytoscape</a> 3 app allowing the user to get and display domain information for proteins
using the Conserved Domains Database. The domain information is stored in the nodes table
and displayed through the Results panel. If the PDB identifier of the protein(s) is also
available and structureViz is also installed, it will also open up the PDB structure of
the protein(s) using Chimera via structureViz.
</p><p>
<a name="contents"><h4 class="ul">Contents</h4></a>
<ol class="dotted">
<li class="dotted"><a href="#install">Installation</a></li>
<li class="dotted"><a href="#structure_panel">The Open Structure Panel</a></li>
<li class="dotted"><a href="#cdd_panel">CDD Panel</a></li>
<li class="dotted"><a href="#menus"><i>CDDApp</i> menus</a>
<ol class="dotted">
<li class="dotted"><a href="#menus_top">Top-level menus</a></li>
<li class="dotted"><a href="#menus_context">Context menus</a></li>
</ol>
</li>
<li class="dotted"><a href="#commands"><i>CDDApp</i> Commands</a></li>
</ol>
<table align="right"><tr><td><font size="-1">
[<a href="#contents" class="nounder">Contents</a>]
[<a href="#top" class="nounder">Top</a>]
</font></td></tr></table>
<h4 class="ul"><a name="install">1. Installation</a></h4>
<ol>
<li>If you haven't already done so,
<a href="http://www.cgl.ucsf.edu/chimera/download.html">download</a>
and install UCSF Chimera.</li>
<li>
Install <i>CDDApp</i> from the Cytoscape Apps Manager (see the
<b class="menuItem">Apps Manager</b>
option in the <b class="menuItem">Apps</b> menu;
<i>CDDApp</i> is listed under the
<b class="menuLabel">Analysis Plugins</b> category).
</li>
<li>Also install structureViz through the <b class="menuItem">Apps</b> menu
if it is not in Cytoscape.</li>
<li>Now CDDApp actions should be available in the Cytoscape
<b class="menuItem">Apps</b> menu and network and node context menus.</li>
</ol>
<table align="right"><tr><td><font size="-1">
[<a href="#contents" class="nounder">Contents</a>]
[<a href="#top" class="nounder">Top</a>]
</font></td></tr></table>
<h4 class="ul"><a name="structure_panel">
2. The Open Structure Panel
</a></h4>
<p>
The Open Structure Panel is a panel that allows the user to open the protein structure of a node if it has a PDB ID.
For this feature to work, structureViz must first be installed. Each node has a sub-panel in Open Structure Panel, each
sub-panel contains a drop-down list to select the protein (in the instance there is more than one protein for the node),
and a button <b>Open Structure</b> that opens the structure in Chimera. Once the structure is opened, a list will appear in
the sub-panel containing domains from CDD. Clicking on the item of the list will highlight the domain in Chimera. Click on
the <b>Close Structure</b> button closes the structure in Chimera.
</p>
<table align="right"><tr><td><font size="-1">
[<a href="#contents" class="nounder">Contents</a>]
[<a href="#top" class="nounder">Top</a>]
</font></td></tr></table>
<h4 class="ul"><a name="cdd_panel">3. CDD Panel
</a></h4>
<p>The CDD Panel is in the Results Panel of Cytoscape, which can be open through the top-level menu View→Show Results Panel.
The CDD Panel is filled by selecting one or more nodes in the network. For each node, domain information appears in the following format:</p>
<ul>
<li>Node: The name of the node</li>
<li>Protein: The name of the protein</li>
<li>Table: A table containing domain information, listed in three columns:
<ul>
<li>Domain Name: Identifier of the domain. For domains curated by CDD, the identifier can be clicked to open up a link to get more information about the domain.</li>
<li>Domain Type: Type of domain.</li>
<li>Domain Range: Residues in the domain.</li>
</ul>
</li>
</ul>
<table align="right"><tr><td><font size="-1">
[<a href="#contents" class="nounder">Contents</a>]
[<a href="#top" class="nounder">Top</a>]
</font></td></tr></table>
<h4 class="ul">
<a name="menus">4. <i>CDDApp</i> menus
</a></h4>
<p><i>CDDApp</i> provides two similar sets of menus, one under the
<b class="menuItem">Apps→cddApp</b> top-level menu
and the other as part of
the context menus accessed by mouse
<b class=mouse">right-click</b> in the Cytoscape network or nodes.
</p>
<h4 class="ul"><a name="menus_top">
4.1 Top-level menus
</a></h4>
<dl>
<dt><b class="menuItem">Load CDD Domains for Network</b></dt>
<dd>
Load domain information from CDD for every node in the network. The user should choose the column to use as protein identifiers. The identifiers can be GI, uniprot or PDB. Multiple identifiers can be specified, and can be in a comma-separated String or a List of String(s). (Note: downloading information from CDD can take a long time, if you only need to load CDD information for a select number of nodes use <b>Load CDD Domains for selected Node(s).</b>
</dd>
<dt><b class="menuItem">Load CDD Domains for selected Node(s)</b></dt>
<dd>
Similar to <b>Load CDD Domains for Network</b>, except only nodes that have been selected will be loaded.
</dd>
<dt><b class="menuItem">Open Structure Panel</b></dt>
<dd>
Opens Structure Panel.
</dd>
</dl>
<h4 class="ul"><a name="menus_context">
4.2 Context menus
</a></h4>
<p>Cytoscape context menus can be activated by right-clicking on the network.
The network context menu contains <b>Load CDD Domains for selected Node(s)</b>, which functions exactly the same way as the equivalent menu item in the top-level menu.
The node context menu contains the item <b>Load CDD Domains for Node</b>, which functions exactly the same as <b>Load CDD Domains for selected Node(s)</b> but does this for the single node being clicked on.
</p>
<table align="right"><tr><td><font size="-1">
[<a href="#contents" class="nounder">Contents</a>]
[<a href="#top" class="nounder">Top</a>]
</font></td></tr></table>
<table align="right"><tr><td><font size="-1">
[<a href="#contents" class="nounder">Contents</a>]
[<a href="#top" class="nounder">Top</a>]
</font></td></tr></table>
<h4 class="ul"><a name="commands">
5. <i>CDDApp</i> Commands
</a></h4>
<p>In order to facilitate the use of <i>CDDApp</i>, the
<i>CDDApp</i> app exports a number of commands. These
commands may be used by other apps, or as part of scripts.
</p>
<dl>
<dt><a name="createSet"><i class="menuLabel">cddApp loadCDDDomains4network</i></a></dt>
<dd>
<p>Loads domain information for all nodes in network from CDD.</p>
<div style="margin-top: 5px"><b style="font-size:90%">Arguments</b>:
<ul>
<li><b>loadColumn</b>=<i>ListSingleSelection</i>: The column to use as identifiers for querying CDD.</li>
</ul>
</div>
</dd>
<dt><a name="union"><i class="menuLabel">cddApp loadCDDDomains4selectedNodes</i></a></dt>
<dd>
<p>Loads domain information for selected nodes in network from CDD.</p>
<div style="margin-top: 5px"><b style="font-size:90%">Arguments</b>:
<ul>
<li><b>loadColumn</b>=<i>ListSingleSelection</i>: The column to use as identifiers for querying CDD.</li>
</ul>
</div>
</dd>
<dt><a name="intersect"><i class="menuLabel">cddApp structurePanel</i></a></dt>
<dd>
<p>Open Open Structure Panel.</p>
</dd>
</dl>
<table align="right"><tr><td><font size="-1">
[<a href="#contents" class="nounder">Contents</a>]
[<a href="#top" class="nounder">Top</a>]
</font></td></tr></table>
<p><hr align=left></p>
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