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Andreas Prlic
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trying to correctly display image in table
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‎README.md‎

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biojava3-tutorial
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BioJava 3 tutorial
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=================
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A tutorial for BioJava 3.
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A brief introduction into BioJava 3.
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==
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The goal of this tutorial is to provide an educational introduction into
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some of the features that are provided by BioJava. Please check also the [BioJava Cookbook](http://biojava.org/wiki/BioJava:CookBook3.0) for a
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collection of many examples of what is possible and how to do things.
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The goal of this tutorial is to provide an educational introduction into some of the features that are provided by BioJava.
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At the moment this tutorial is still under development. Please check the [BioJava Cookbook](http://biojava.org/wiki/BioJava:CookBook3.0) for a more comprehensive collection of many examples of what is possible with BioJava and how to do things.
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## Index
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Book 1: [The Protein Structure modules](structure/README.md)
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<script type="text/javascript" src="JSmol.min.js"></script>
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<script type="text/javascript">
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// 1/21/2013 10:54:15 PM -- adds image handling
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var jmolApplet0; // set up in HTML table, below
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// logic is set by indicating order of USE -- default is HTML5 for this test page, though
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var use = "HTML5" // JAVA HTML5 WEBGL IMAGE are all otions
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var s = document.location.search;
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// Developers: The debugCode flag is checked in j2s/core/core.z.js,
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// and, if TRUE, skips loading the core methods, forcing those
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// to be read from their individual directories. Set this
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// true if you want to do some code debugging by inserting
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// System.out.println, document.title, or alert commands
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// anywhere in the Java or Jmol code.
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Jmol.debugCode = (s.indexOf("debugcode") >= 0);
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jmol_isReady = function(applet) {
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Jmol._getElement(applet, "appletdiv").style.border="1px solid blue"
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}
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var xxxx = document.location.search
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if (xxxx.length == 5 || xxxx.length == 0) {
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xxxx = (xxxx + "?1crn").substring(1,5)
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script = 'h2oOn=true;set animframecallback "jmolscript:if (!selectionHalos) {select model=_modelNumber}";'
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+'set errorCallback "myCallback";'
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+'set defaultloadscript "isDssp = false;set defaultVDW babel;if(!h2oOn){display !water}";'
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+'set zoomlarge false;set echo top left;echo loading XXXX...;refresh;'
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+'load "http://www.rcsb.org/pdb/files/XXXX.pdb";set echo top center;echo XXXX;'
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+'spacefill off;wireframe off;cartoons on;color structure;'
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script = script.replace(/XXXX/g, xxxx)
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} else {
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script = unescape(xxxx.substring(1))
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}
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var Info = {
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width: 450,
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height: 450,
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debug: false,
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color: "white",
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addSelectionOptions: false,
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serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
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use: "HTML5",
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j2sPath: "j2s",
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readyFunction: jmol_isReady,
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script: script,
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//jarPath: "java",
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//jarFile: (useSignedApplet ? "JmolAppletSigned.jar" : "JmolApplet.jar"),
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//isSigned: useSignedApplet,
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//disableJ2SLoadMonitor: true,
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disableInitialConsole: true
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//defaultModel: "$dopamine",
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//console: "none", // default will be jmolApplet0_infodiv
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}
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</script>
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<script type="text/javascript">
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jmolApplet0 = Jmol.getApplet("jmolApplet0", Info)
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</script>

‎structure/chemcomp.md‎

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### How does BioJava decide what groups are amino acids?
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BioJava utilizes the Chem. Comp. Dictionary to achieve a chemically correct representation of each group. To make it clear how this can work, let's take a look at how [Selenomethionine](http://en.wikipedia.org/wiki/Selenomethionine) and water is dealt with:
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<table>
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<tr><td>
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![Selenomethionine is a naturally occurring amino acid containing selenium](img/143px-Selenomethionine-from-xtal-3D-balls.png "Selenomethionine is a naturally occurring amino acid containing selenium source: wikipedia")
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![Selenomethionine is a naturally occurring amino acid containing selenium](img/143px-Selenomethionine-from-xtal-3D-balls.png?raw=true "Selenomethionine is a naturally occurring amino acid containing selenium source: wikipedia")
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</td>
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<td>Selenomethionine is a naturally occurring amino acid containing selenium source: wikipedia
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</td>
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</tr>
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</table>
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BioJava utilizes the Chem. Comp. Dictionary to achieve a chemically correct representation of each group. To make it clear how this can work, let's take a look at how [Selenomethionine](http://en.wikipedia.org/wiki/Selenomethionine) and water is dealt with:
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<pre>

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