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<!DOCTYPE html> <html lang="en"> <head> <meta charset=utf-8"/> <link rel="stylesheet" href="default.css" type="text/css" /> <meta name="description" content="jV is a program to display molecular graphics of proteins and nucleic acids. It also can move the molecular graphic interactively with mouse actions or command directives." /> <meta name="keywords" content="jV,PDBj,molecular viewer" /> <title>jV - interactive molecular viewer</title> </head> <body> <div id="top"></div> <div id="langlink"> <a href="index_j.html">[Japanese]</a> </div> <div id="title"> <img src="/jv/w/images/jV.png" alt="jV molecular viewer" title="jV molecular viewer"/> <h1>PDBjViewer (jV)</h1> </div> <p>[<a href="#intro">Introduction</a> | <a href="#guide">Basic Usage</a> | <a href="#manual">Manual</a> | <a href="#display">Graphics Examples</a> | <a href="#download">Download & Install</a> | <a href="#ackno">Acknowledgment</a> | <a href="/jv/wiki/">jV wiki</a> | <a href="/">PDBj Home</a> ]</p> <hr /> <div id="intro" class="chapter"> <h2>Introduction</h2> PDBjViewer (jV, for short) is a program to display molecular graphics of proteins and nucleic acids. jV supports the following features: <ul> <li>jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.</li> <li>Of course, jV can read and display the traditional PDB format files, too.</li> <li>RasMol-like usability.</li> <li>jV can process more than one molecules.</li> <li>jV can display polygons specified by XML. (<a href="/eF-site/schema/polygon12.xsd">XML Schema for polygons</a> is available.)</li> <li>Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.</li> <li>Animation can be realized. (Each frame of an animation is made of a single MODEL entity of the traditional PDB format file.) <li>jV runs on the Java Runtime Environment (<a href="http://java.sun.com/j2se/">JRE</a>) so that it can work as a stand-alone application.</li> <li>The graphics of jV is based on OpenGL (JOGL), thereby producing <a href="#display">fairly beautiful</a> pictures.</li> </ul> <nav>[<a href="#top">Page top</a> | <a href="#intro" class="current">Introduction</a> | <a href="#guide">Basic Usage</a> | <a href="#manual">Manual</a> | <a href="#display">Graphics Examples</a> | <a href="#download">Download & Install</a> | <a href="#ackno">Acknowledgment</a> | <a href="/jv/wiki/">jV wiki</a> | <a href="/">PDBj Home</a> ]</nav> <hr /> </div> <div id="guide" class="chapter"> <h2>Basic Usage</h2> <p> You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table: </p> <table id="tbl_guide"> <tr> <th rowspan="2">Action</th><th colspan="2">Mouse Operation</th> </tr> <tr> <th>Windows, Linux</th><th>Mac OS X</th> </tr> <tr> <td>rotate around X (horizontal) axis<br />rotate around Y (vertical) axis</td> <td>left drag</td> <td>drag</td> </tr> <tr> <td>rotate around Z (anteroposterior) axis</td> <td>Shift + right drag (move horizontally)</td> <td>Shift + Command + drag (move horizontally)</td> </tr> <tr> <td>translate along X axis (holizontally)<br />translate along Y axis (vertically)</td> <td>right drag</td> <td>Command + drag</td> </tr> <tr> <td>translate along Z axis (zoom in/out)</td> <td>Shift + left drag</td> <td>Shift + drag</td> </tr> </table> <p> Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application. </p> <table id="tbl_guide_menu"> <tr> <td><a href="manual/images/jv_menu_win.png"><img src="manual/images/jv_menu_win.png" alt="The screenshot of the jV application window for Windows" width="250"/></a></td> <td><a href="manual/images/jv_menu_mac.png"><img src="manual/images/jv_menu_mac.png" alt="The screenshot of the jV application window for Mac" width="250"/></a></td> </tr> <tr id="tbl_guide_menu_caption"> <td>Application window for Windows</td> <td>Application window for Mac</td> </tr> </table> <p> Basic menu operations are following (see also <a href="/jv/wiki/GUI">jV wiki</a> for details): </p> <table id="tbl_guide_basicmenu"> <tr> <th>Operations</th> <th>Menu location</th> </tr> <tr> <td>Save a static image</td> <td>[File]-[Save]-[PNG/JPEG]</td> </tr> <tr> <td>Change the expression format</td> <td>[File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&Stick/Ribbons/Cartoon]</td> </tr> <tr> <td>Change the color</td> <td>[File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]</td> </tr> </table> <p> To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation. </p> <p> See also the following links for details: </p> <nav>[<a href="#top">Page top</a> | <a href="#intro">Introduction</a> | <a href="#guide" class="current">Basic Usage</a> | <a href="#manual">Manual</a> | <a href="#display">Graphics Examples</a> | <a href="#download">Download & Install</a> | <a href="#ackno">Acknowledgment</a> | <a href="/jv/wiki/">jV wiki</a> | <a href="/">PDBj Home</a> ]</nav> <hr /> </div> <div id="manual" class="chapter"> <h2>Manual</h2> <ul id="ul_guide"> <li><a href="/eF-site/jV/jV_manual.html">English, html version</a></li> <li><a href="/jv/wiki/How_to_use">English, wiki version</a></li> <li><a href="/jv/manual/index_ja.html">Japanese, html version</a></li> </ul> <nav>[<a href="#top">Page top</a> | <a href="#intro">Introduction</a> | <a href="#guide">Basic Usage</a> | <a href="#manual" class="current">Manual</a> | <a href="#display">Graphics Examples</a> | <a href="#download">Download & Install</a> | <a href="#ackno">Acknowledgment</a> | <a href="/jv/wiki/">jV wiki</a> | <a href="/">PDBj Home</a> ]</nav> <hr /> </div> <div id="display" class="chapter"> <h2>Graphics Examples</h2> <table id="tbl_display"> <tr> <td> <a href="images/spacefill.jpg"> <img src="images/spacefill.jpg" alt="Spacefill expression" /> </a> </td> <td> <a href="images/cartoon.jpg"> <img src="images/cartoon.jpg" alt="Cartoon expression" /> </a> </td> <td> <a href="images/surface.jpg"> <img src="images/surface.jpg" alt="Molecular surface" /> </a> </td> <td> <a href="images/edmap.jpg"> <img src="images/edmap.jpg" alt="Electron density" /> </a> </td> </tr> <tr id="tbl_display_caption"> <td>Spacefill expression</td> <td>Cartoon expression</td> <td>Molecular surface</td> <td>Electron density</td> </tr> </table> <nav>[<a href="#top">Page top</a> | <a href="#intro">Introduction</a> | <a href="#guide">Basic Usage</a> | <a href="#manual">Manual</a> | <a href="#display" class="current">Graphics Examples</a> | <a href="#download">Download & Install</a> | <a href="#ackno">Acknowledgment</a> | <a href="/jv/wiki/">jV wiki</a> | <a href="/">PDBj Home</a> ]</nav> <hr /> </div> <div id="download" class="chapter"> <h2>Download & Install</h2> <ul> <li><a href="#download_envstandalone">Required environment</a></li> <li><a href="#download_trouble">Trouble shoooting</a></li> </ul> <div id="download_envstandalone" class="section"> <h3>Required environment</h3> <p> To run the jV application, it is necessary to install Java Runtime Environment (JRE) in advance. Please access the <a href="https://www.java.com/ja/" onclick="window.open(this.href,'Java');return false">Java website</a> to download and install it. </p> </p> <p>The latest version is <b>4.5.10</b>. <ul> <li><span class="del">jnlp file [Java Web Start version (recommended)]</span> -> we finished to provide the web start version. Please download the binary below.</li> <li><a href="/jv/download/binary">Executable JAR file</a></li> </ul> <p> If you ever want to modify and customize the jV program, please download the <a href="/jv/download/source">source file</a>. </p> </div> <div id="download_applet" class="section"> <h3>Documents for applet settings</h3> <p> In case you are to applet settings, you may refer the <a href="/jv/wiki/Use_jV_with_applet_launcher">jV wiki</a>. </p> </div> <div id="download_trouble" class="section"> <h3>Trouble shoooting</h3> <p> When you hit upon some troubles in installing or viewing molecules, refer <a href="/jv/wiki/Trouble_shooting">jV wiki - Trouble Shooting</a> (in English) or <a href="/jv/manual/trouble_ja.html">jV Usage manual - Trouble Shooting</a> (in Japanese). </p> </div> <nav>[<a href="#top">Page top</a> | <a href="#intro">Introduction</a> | <a href="#guide">Basic Usage</a> | <a href="#manual">Manual</a> | <a href="#display">Graphics Examples</a> | <a href="#download" class="current">Download & Install</a> | <a href="#ackno">Acknowledgment</a> | <a href="/jv/wiki/">jV wiki</a> | <a href="/">PDBj Home</a> ]</nav> <hr /> </div> <div id="ackno"> <h2>Acknowledgment</h2> <p> The jV program was developed by <a href="http://www.sb.ecei.tohoku.ac.jp/" onclick="window.open(this.href,'tohokuu');return false">Kengo Kinoshita</a> (<a href="https://www.is.tohoku.ac.jp/en/" onclick="window.open(this.href,'tohokuu');return false">Graduate School of Information Sciences</a>, <a href="http://www.tohoku.ac.jp/en/" onclick="window.open(this.href,'tohokuu');return false">Tohoku University</a>) and Haruki Nakamura (<a href="http://www.protein.osaka-u.ac.jp/en/" onclick="window.open(this.href,'ipr');return false">Institute for Protein Research</a> (IPR), <a href="https://www.osaka-u.ac.jp/en" onclick="window.open(this.href,'osakauniv');return false">Osaka University</a>) as one of activity of <a href="https://pdbj.org/">Protein Data Bank Japan</a> (PDBj), with the support from <a href="https://biosciencedbc.jp/en/" onclick="window.open(this.href,'nbdc');return false">JST-NBDC</a> and <a href="http://www.protein.osaka-u.ac.jp/en/" onclick="window.open(this.href,'ipr');return false">Institute for Protein Research</a>, <a href="https://www.osaka-u.ac.jp/en" onclick="window.open(this.href,'osakauniv');return false">Osaka University</a>. </p> <nav>[<a href="#top">Page top</a> | <a href="#intro">Introduction</a> | <a href="#guide">Basic Usage</a> | <a href="#manual">Manual</a> | <a href="#display">Graphics Examples</a> | <a href="#download">Download & Install</a> | <a href="#ackno" class="current">Acknowledgment</a> | <a href="/jv/wiki/">jV wiki</a> | <a href="/">PDBj Home</a> ]</nav> <hr /> </div> <a href="/"><img src="/images/pdbj2.png" alt="PDBj Home" title="PDBj Home"/></a> </body> <html>