Merge branch 'symmetry' of https://github.com/lafita/biojava-tutorial into symmetry

lafita · lafita · commit 70a9a06c04c8 · 2015-08-05T16:56:47.000+02:00
diff --git a/structure/symmetry.md b/structure/symmetry.md
@@ -7,16 +7,89 @@ BioJava can be used to detect, analyze, and visualize **symmetry** and
 
 ## Quaternary Symmetry
 
-![PDB ID 1G63](https://raw.github.com/rcsb/symmetry/master/docu/img/1G63.jpg)
+The **quaternary symmetry** of a structure defines the relations between 
+its individual chains or groups of chains. For a more extensive explanation 
+about symmetery visit the [PDB help page]
+(http://www.rcsb.org/pdb/staticHelp.do?p=help/viewers/jmol_symmetry_view.html).
+
+In the **quaternary symmetry** detection problem, we are given a set of chains
+with its `Atom` coordinates and we are asked to find the higest overall symmetry that
+relates them. The solution is divided into the following steps:
+
+1. First, we need to identify the chains that are identical (or similar
+in the pseudo-symmetry case). For that, we perform a pairwise alignment of all
+chains and determine **clusters of identical chains**.
+2. Next, we reduce the each chains to a single point, its **centroid** (center of mass).
+3. After that, we try different **symmetry relations** to superimpose the chain centroids 
+and obtain their RMSD.
+4. At last, based on the parameters (cutoffs), we determine the **overall symmetry** of the
+structure, with the symmetry relations obtained in the previous step.
+5. In case of asymmetric structure, we discard combinatorially a number of chains and try
+to detect any **local symmetries** present.
+
+The **quaternary symmetry** detection algorithm is implemented in the biojava class
+[QuatSymmetryDetector](http://www.biojava.org/docs/api/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector).
+An example of how to use it programatically is shown below:
+
+```java
+//First download the structure in the biological assembly form
+Structure s;
+
+//Set some parameters if needed different than DEFAULT - see descriptions
+QuatSymmetryParameters parameters = new QuatSymmetryParameters();
+parameters.setVerbose(true); //print information
+
+//Instantiate the detector and calculate symmetry
+CalcBioAssemblySymmetry calc = new CalcBioAssemblySymmetry(s, parameters);
+QuatSymmetryDetector detector = calc.orient();
+
+//Calculate and return global and local results
+List<QuatSymmetryResults> globalResults = detector.getGlobalSymmetry();
+List<List<QuatSymmetryResults>> localResults = detector.getLocalSymmetries();
+
+```
+
+The `QuatSymmetryResults` object contains all the information of the symmetry.
+This object will be used later to obtain axes of symmetry, point group name,
+stoichiometry or even display the results in Jmol.
 
 ### Global Symmetry
 
+In **global symmetry** all chains have to be part of the symmetry description.
+
+#### Point Group
+
+In a **point group** a single or multiple rotation axes define the overall symmetry
+operations, with the property that all the axes coincide in the same point.
+
+![PDB ID 1G63](img/1G63.jpg)
+
+#### Helical
+
+In **helical** symmetry there is a single axis with rotation and translation
+components.
+
+![PDB ID 4UDV](img/symm_helical.png)
 
 ### Local Symmetry
 
+In **local symmetry** a number of chains is left out, so that the symmetry
+only applies to a subset of chains.
+
+![PDB ID 4F88](img/symm_local.png)
 
 ### Pseudo-Symmetry
 
+In **pseudo-symmetry** the chains related by the symmetry are not completely
+identical, but they share a sequence similarity above the pseudo-symmetry 
+similarity threshold. 
+If we consider hemoglobin, at a 95% sequence identity threshold the alpha and 
+beta subunits are considered different, which correspond to an A2B2 stoichiometry 
+and a C2 point group. At the structural similarity level, all four chains are 
+considered homologous (~45% sequence identity) with an A4 pseudostoichiometry and 
+D2 pseudosymmetry. 
+
+![PDB ID 4HHB](img/symm_pseudo.png)
 
 ## Internal Symmetry
 
