Update crystal-contacts.md

josemduarte · josemduarte · commit f0ec3f23ef59 · 2014-08-27T22:49:04.000+02:00
diff --git a/structure/crystal-contacts.md b/structure/crystal-contacts.md
@@ -4,9 +4,6 @@
 
 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
 
@@ -21,11 +18,15 @@ This code snippet will produce a list of all non-redundant interfaces present in
 			
 		CrystalBuilder cb = new CrystalBuilder(structure);
 		
+		// 6 is the distance cutoff to consider 2 atoms in contact
 		StructureInterfaceList interfaces = cb.getUniqueInterfaces(6);
+		
+		System.out.println("The crystal contains "+interfaces.size()+" unique interfaces");
 
+		// this calculates the buried surface areas of all interfaces and sorts them by areas
 		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
+		// we can get the largest interface in the crystal and look at its area
 		interfaces.get(1).getTotalArea();
 
 ```
