The simplest way to load a PDB file is by using the [StructureIO](http://www.biojava.org/docs/api/org/biojava3/structure/StructureIO.html) class.

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

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

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

By default BioJava is using the PDB file format for parsing data. In order to switch it to use mmCIF, we can take control over the underlying [AtomCache](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/util/AtomCache.html) which manages your PDB (and btw. also SCOP, CATH) installations.

AtomCache cache = new AtomCache();

cache.setUseMmCif(true);

// and let's count how many chains are in this structure.

System.out.println(structure.getChains().size());

As you can see, the AtomCache will again download the missing mmCIF file for 4HHB in the background.

If you want to learn how to use the BioJava mmCIF parser to populate your own data structure, let's first take a look this lower-level code:

InputStream inStream = new FileInputStream(fileName);

MMcifParser parser = new SimpleMMcifParser();

// now get the protein structure.

Structure cifStructure = consumer.getStructure();

The parser operates similar to a XML parser by triggering "events". The [SimpleMMcifConsumer](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html) listens to new categories being read from the file and then builds up the BioJava data model.