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andreasprlic merged 13 commits into from
Aug 6, 2015
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Symmetry Chapter #6

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Update Structure readme
lafita Aug 5, 2015
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Symmetry chapter template
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Symmetry images
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Explain quaternary symmetry detection
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CeSymm description
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Detection of Protein Symmetry and Pseudo-symmetry using BioJava
Protein Symmetry using BioJava
================================================================

This chapter is still under construction. See the [protein symmetry](https://github.com/rcsb/symmetry) project for more information for now.
BioJava can be used to detect, analyze, and visualize **symmetry** and
**pseudo-symmetry** in the quaternary (biological assembly) and tertiary
(internal) structural levels.

## Quaternary Symmetry

BioJava can be used to
- Detect, analyze, and visualize **protein symmetry**
- Detect symmetry in **biological assemblies**

![PDB ID 1G63](https://raw.github.com/rcsb/symmetry/master/docu/img/1G63.jpg)

- Detect **internal pseudo-symmetry** in protein chains
### Global Symmetry


### Local Symmetry


### Pseudo-Symmetry


## Internal Symmetry

**Internal symmetry** refers to the symmetry present in a single chain, that is,
the tertiary structure. The algorithm implemented in biojava to detect internal
symmetry is called **CE-Symm**.

### CE-Symm

`CeSymm`

###

![SCOP ID d1jlya1](https://raw.github.com/rcsb/symmetry/master/docu/img/CeSymmScreenshotd1jlya1.png)

- Visualize results in [Jmol](http://www.jmol.org)