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Andreas Prlic
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working on tutorial
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‎structure/README.md‎

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## Index
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This tutorial is split into several chapters.
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Chapter 1 - The [BioJava data model](structure-data-model.md) for the representation of macromolecular structures.
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Chapter 1 - Quick [Installation](installation.md)
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Chapter 2 - First Steps
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Chapter 3 - The [data model](structure-data-model.md) for the representation of macromolecular structures.
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Chapter 4 - Local installations of PDB
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Chapter 5 - The [Chemical Component Dictionary](chemcomp.md)
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Chapter 6 - How to [work with mmCIF/PDBx files](mmcif.md)
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Chapter 7 - SEQRES and ATOM records
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Chapter 8 - Protein Structure Alignments
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Chapter 9 - Biological Assemblies
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Chapter 10 - Protein Symmetry
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Chapter 2 - The [Chemical Component Dictionary](chemcomp.md)
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Chapter X - How to [work with mmCIF/PDBx files](mmcif.md).
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‎structure/chemcomp.md‎

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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?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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<pre>
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Structure structure = StructureIO.getStructure("1A62");
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As you can see, although MSE is flaged as HETATM in the PDB file, BioJava still represents it correctly as an amino acid. They key is that the [definition file for MSE](http://www.rcsb.org/pdb/files/ligand/MSE.cif) flags it as "L-PEPTIDE LINKING", which is being used by BioJava.
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<table>
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<tr><td>
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<img src="img/143px-Selenomethionine-from-xtal-3D-balls.png?raw=true" alt="Selenomethionine is a naturally occurring amino acid containing selenium" />
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</td>
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<td>
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Selenomethionine is a naturally occurring amino acid containing selenium. It has the ID <a href="http://www.rcsb.org/pdb/files/ligand/MSE.cif">MSE</a> in the Chemical Component Dictionary. (image source: <a href="http://en.wikipedia.org/wiki/File:Selenomethionine-from-xtal-3D-balls.png">wikipedia</a>)
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</td>
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</tr>
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</table>
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### How to access Chemical Component definitions
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Bye default BioJava ships with a minimal representation of standard amino acids, however if you want to parse the whole PDB archive, it is good to tell the library to either

‎structure/mmcif.md‎

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BioJava provides you with both a mmCIF parser and a data model that reads PDB and mmCIF files into a biological and chemically meaningful data model (BioJava supports the [Chemical Components Dictionary](http://www.wwpdb.org/ccd.html)). If you don't want to use that data model, you can still use BioJava's file parsers, and more on that later, let's start first with the most basic way of loading a protein structure.
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## Quick Installation
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Before we start, just one quick paragraph of how to get access to BioJava.
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BioJava is open source and you can get the code from [Github](https://github.com/biojava/biojava), however it might be easier this way:
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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We are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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<dependencies>
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...
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<dependency>
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<!-- This imports the latest SNAPSHOT builds from the protein structure modules of BioJava
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-->
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-structure</artifactId>
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<version>3.0.7-SNAPSHOT</version>
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</dependency>
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<!-- other biojava jars as needed -->
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</dependencies>
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```
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If you run 'mvn package' on your project, the BioJava dependencies will be automatically downloaded and installed for you.
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## First steps
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‎structure/structure-data-model.md‎

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All structure objects contain one or more "models". That means also X-ray structures contain an "virtual" model which serves as a container for the chains. The most common way to access chains will be via
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<pre>
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List<Chain>chains = structure.getChains();
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List < Chain > chains = structure.getChains();
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</pre>
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This works for both NMR and X-ray based structures and by default the first model is getting accessed.

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