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andreasprlic merged 7 commits into from
Aug 28, 2014
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New tutorials on contacts and crystal interfaces #1

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New tutorial chapter
josemduarte Aug 27, 2014
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Update crystal-contacts.md
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New tutorial on contact maps
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Update crystal-contacts.md
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josemduarte committed Aug 27, 2014
commit f0ec3f23ef59c06514689c8a31185a7238f18bb7
9 changes: 5 additions & 4 deletions structure/crystal-contacts.md
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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

Expand All @@ -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();

```
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