First Steps

The simplest way to load a PDB file is by using the [StructureIO](http://www.biojava.org/docs/api/org/biojava/nbio/structure/StructureIO.html) class.

-DPDB_DIR=/wherever/you/want/

</pre>

Talking about startup properties, it is also good to mention the fact that many PDB entries are large molecules and the default 64k memory allowance for Java applications is not sufficient in many cases. BioJava contains several built-in caches which automatically adjust to the available memory. As such, the more memory you grant your Java applicaiton, the better it can utilize the caches and the better the performance will be. Change the maximum heap space of your Java VM with this startup parameter:

</tr>

</table>

By default many people work with the *asymmetric unit* of a protein. However for many studies the correct representation to look at is the *biological assembly* of a protein. You can request it by calling

This topic is important, so we dedicated a [whole chapter](bioassembly.md) to it.

BioJava provides a number of algorithms and visualisation tools that you can use to further analyse the structure, or look at it. Here a couple of suggestions for further reads:

+ [The BioJava Cookbook for protein structures](http://biojava.org/wiki/BioJava:CookBook#Protein_Structure)

+ How does BioJava [represent the content](structure-data-model.md) of a PDB/mmCIF file?

+ [How to work with Groups (AminoAcid, Nucleotide, Hetatom)](http://biojava.org/wiki/BioJava:CookBook:PDB:groups)

Navigation:

[Home](../README.md)

| Chapter 2 : First Steps

Prev: [Chapter 1 : Installation](installation.md)