New tutorial chapter

biojava · andreasprlic · Aug 28, 2014 · Aug 27, 2014 · Aug 27, 2014 · Aug 28, 2014
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+# How to calculate all crystal contacts in a PDB structure
+
+## Why crystal contacts?
+
+A protein structure is determined by X-ray diffraction by producing a crystal - an infinite lattice of molecules - of the protein. Thus the end result of the diffraction experiment is a crystal lattice and not just a single molecule. However the PDB file only contains the coordinates of the Asymmetric Unit, defined as the minimum unit needed to reconstruct the full crystal using symmetry operators. 
+
+[here](http://www.wwpdb.org/news/news_2013.html#22-May-2013)
+
+
+
+## Getting the set of unique contacts in the crystal lattice
+
+This code snippet will produce a list of all non-redundant interfaces present in the crystal lattice of PDB entry [1SMT](http://www.rcsb.org/pdb/explore.do?structureId=1SMT):
+
+```java
+		AtomCache cache = new AtomCache();
+
+		StructureIO.setAtomCache(cache); 
+
+		Structure structure = StructureIO.getStructure("1SMT");
+
+		CrystalBuilder cb = new CrystalBuilder(structure);
+
+		StructureInterfaceList interfaces = cb.getUniqueInterfaces(6);
+
+		interfaces.calcAsas(3000, 1, -1);
+
+		// now interfaces are sorted by areas, we can get the largest interface in the crystal and look at its area
+		interfaces.get(1).getTotalArea();
+
+```
+
+An interface is defined here as any 2 chains with at least a pair of atoms within the given distance cutoff (6 A in the example above)
+
+
+