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CeSymm description
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‎structure/symmetry.md‎

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@@ -62,7 +62,7 @@ In **global symmetry** all chains have to be part of the symmetry description.
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In a **point group** a single or multiple rotation axes define the overall symmetry
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operations, with the property that all the axes coincide in the same point.
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![PDB ID 1G63](img/1G63.jpg)
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![PDB ID 1VYM](img/symm_pg.png)
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#### Helical
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In **pseudo-symmetry** the chains related by the symmetry are not completely
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identical, but they share a sequence similarity above the pseudo-symmetry
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similarity threshold.
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similarity threshold.
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If we consider hemoglobin, at a 95% sequence identity threshold the alpha and
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beta subunits are considered different, which correspond to an A2B2 stoichiometry
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and a C2 point group. At the structural similarity level, all four chains are
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### CE-Symm
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`CeSymm`
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As the name of the algorithm explicitly states, **CE-Symm** uses a **CE** alignment
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of the structure chain to itself, disabling the identity alignment (the diagonal of
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the **DotPlot** representation of a structure alignment). This allows the identification
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of alternative self-alignments, which are related to symmetry and/or structural repeats
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inside the chain.
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By a procedure called **refinement**, the subunits of the chain that are part of the symmetry
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are defined and a **multiple alignment** is created. This process can be thought as to
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divide the chain into other subchains, and then superimposing each subchain to each other to
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create a multiple alignment of the subunits, respecting the symmetry axes.
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The **internal symmetry** detection algorithm is implemented in the biojava class
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[CeSymm](http://www.biojava.org/docs/api/org/biojava/nbio/structure/symmetry/internal/CeSymm).
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It implements the both [Structural Alignment](alignment.md) interfaces, so it works programatically
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like any of the structural alignment algorithms, and returns one of the structure alignment
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[Data Models](alignment-data-model.md).
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```java
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//Prepare the atom input, in a List with a single array
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Atom[] array = StructureTools.getRepresentativeAtomArray(structure);
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List<Atom[]> atoms = new ArrayList<Atom[]>();
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atoms.add(array);
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//Initialize the algorithm
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CeSymm ceSymm = new CeSymm();
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//Choose some parameters
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CESymmParameters params = (CESymmParameters) ceSymm.getParameters();
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params.setRefineMethod(RefineMethod.SINGLE);
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params.setOptimization(true);
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params.setMultipleAxes(true);
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//Run the symmetry analysis - alignment as an output
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MultipleAlignment symmetry = ceSymm.align(atoms, params);
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//Display the results in jmol with the Symmetry GUI
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SymmetryDisplay.display(symmetry, ceSymm.getSymmetryAxes());
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```
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To enable some extra features in the display, a `SymmetryDisplay`
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class has been created, although the `StrucutreAlignmentDisplay`
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and `MultipleAlignmentDisplay` methods can also be used for that
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purpose (they will not show symmetry axes or symmetry menus).
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Lastly, the `SymmetryGUI` class in the **structure-gui** package
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provides a GUI to trigger internal symmetry analysis, equivalent
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to the GUI to trigger structure alignments.
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### Symmetry Display
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The symmetry display is similar to the **quaternary symmetry**, because
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part of the code is shared. See for example this beta-propeller (1U6D),
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where the repeated beta-sheets are connected by a linker forming a C6
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point group internal symmetry:
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![PDB ID 1U6D](img/symm_internal.png)
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###
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![PDB ID 4GCR.2](img/symm_subunits.png)
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![SCOP ID d1jlya1](https://raw.github.com/rcsb/symmetry/master/docu/img/CeSymmScreenshotd1jlya1.png)
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### Hierarchical Symmetry
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![PDB ID 4GCR](img/symm_hierarchy.png)
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## Combined Global Symmetry
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![PDB ID 1VYM](img/symm_combined.png)

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