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

<pre>

public static void main(String[] args){

try {

Structure structure = StructureIO.getBiologicalAssembly("4HHB");

// and let's print out how many atoms are in this structure

System.out.println(StructureTools.getNrAtoms(structure));

} catch (Exception e){

e.printStackTrace();

}

}

</pre>

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 calculate a protein structure alignment using BioJava](http://biojava.org/wiki/BioJava:CookBook:PDB:align)

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

The detection of the groups works really well in connection with the [Chemical Component Dictionary](checmcomp.md), as we will discuss in the next section. Without this dictionary, there can be inconsistencies in particular with chemically modified residues.