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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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Point Group image
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Merge branch 'symmetry' of https://github.com/lafita/biojava-tutorial…
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CeSymm description
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Explain symmetry GUI
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Explain combined quat and internal symmetries
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Explain symmetry GUI
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lafita committed Aug 6, 2015
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36 changes: 24 additions & 12 deletions structure/symmetry.md
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Expand Up @@ -2,8 +2,8 @@ Protein Symmetry using BioJava
================================================================

BioJava can be used to detect, analyze, and visualize **symmetry** and
**pseudo-symmetry** in the quaternary (biological assembly) and tertiary
(internal) structural levels.
**pseudo-symmetry** in the **quaternary** (biological assembly) and tertiary
(**internal**) structural levels.

## Quaternary Symmetry

Expand Down Expand Up @@ -135,8 +135,11 @@ params.setMultipleAxes(true);
//Run the symmetry analysis - alignment as an output
MultipleAlignment symmetry = ceSymm.align(atoms, params);

//Get the axes of symmetry from the aligner
SymmetryAxes axes = ceSymm.getSymmetryAxes();

//Display the results in jmol with the Symmetry GUI
SymmetryDisplay.display(symmetry, ceSymm.getSymmetryAxes());
SymmetryDisplay.display(symmetry, axes);
```

To enable some extra features in the display, a `SymmetryDisplay`
Expand All @@ -157,22 +160,31 @@ point group internal symmetry:

![PDB ID 1U6D](img/symm_internal.png)

#### Hierarchical Symmetry

One additional feature of the **internal symmetry** display is the representation
of hierarchical symmetries and repeats. Contrary to point groups, some structures
have different **levels** of symmetry. That is, the whole strucutre has, e.g. C2
symmetry and, at the same time, each of the two parts has C2 symmetry, but the axes
of both levels are not related by a point group (i.e. they do not cross to a single
point).

A very clear example are the beta-gamma-crystallins, like 4GCR:

![PDB ID 4GCR](img/symm_hierarchy.png)

#### Subunit Multiple Alignment

Another feature of the display is the option to show the **multiple alignment** of
the symmetry related subunits created during the **refinement** process. Search for
the option *Subunit Superposition* in the *symmetry* menu of the Jmol window. For
the previous example the display looks like that:

![PDB ID 4GCR](img/symm_subunits.png)

![PDB ID 4GCR.2](img/symm_subunits.png)



### Hierarchical Symmetry

![PDB ID 4GCR](img/symm_hierarchy.png)


The subunit display highlights the differences and similarities between the symmetry
related subunits of the chain, and helps the user to identify conseved and divergent
regions, with the help of the *Sequence Alignment Panel*.

## Combined Global Symmetry

Expand Down